diff --git a/server/plugins/headless-sync/plugin/src/core-sync-guard.js b/server/plugins/headless-sync/plugin/src/core-sync-guard.js
index adbf0e8..1abf964 100644
--- a/server/plugins/headless-sync/plugin/src/core-sync-guard.js
+++ b/server/plugins/headless-sync/plugin/src/core-sync-guard.js
@@ -1,9 +1,14 @@
 const { Notice } = require("obsidian");
-const fs = require("fs"); // Using fs shim
+const fs = require("fs");
 
+const CORE_PLUGINS_PATH = ".obsidian/core-plugins.json";
+
+// Reads core-plugins.json via the fs shim. When headless sync is active,
+// the shim patches sync: false, so this returns false. When the flag is
+// cleared (user action), this returns the real value.
 function isCoreSyncEnabled() {
   try {
-    const data = fs.readFileSync(".obsidian/core-plugins.json", "utf-8");
+    const data = fs.readFileSync(CORE_PLUGINS_PATH, "utf-8");
     const config = JSON.parse(data);
     return config.sync === true;
   } catch {
@@ -27,11 +32,31 @@ function showConflictWarning(title, message) {
   });
 }
 
-function startCoreSyncWatcher(plugin, api, wsListener) {
+function startCoreSyncGuard(plugin, api, wsListener) {
+  const app = plugin.app;
+  const vaultId = app.vault.getName();
+
+  // Monkey-patch syncPlugin.enable() to clear the shim flag before
+  // Obsidian writes core-plugins.json. This ensures the read transform
+  // doesn't block a user-initiated core sync enable.
+  const syncPlugin = app.internalPlugins.getPluginById("sync");
+  let origEnable = null;
+
+  if (syncPlugin) {
+    origEnable = syncPlugin.enable.bind(syncPlugin);
+
+    syncPlugin.enable = function (...args) {
+      window.__ignisHeadlessSyncActive = false;
+      api.stopSync(vaultId).catch(() => {});
+      return origEnable(...args);
+    };
+  }
+
+  // Watch for core-plugins.json changes via WebSocket.
   let wasEnabled = isCoreSyncEnabled();
 
   const rawHandler = (msg) => {
-    if (msg.type === "modified" && msg.path === ".obsidian/core-plugins.json") {
+    if (msg.type === "modified" && msg.path === CORE_PLUGINS_PATH) {
       handleCoreSyncChange();
     }
   };
@@ -42,9 +67,6 @@ function startCoreSyncWatcher(plugin, api, wsListener) {
     const enabled = isCoreSyncEnabled();
 
     if (enabled && !wasEnabled) {
-      const vaultId = plugin.app.vault.getName();
-
-      api.stopSync(vaultId).catch(() => {});
       showConflictWarning(
         "Headless Sync Stopped",
         "Obsidian Sync has been enabled. Headless Sync has been automatically " +
@@ -59,11 +81,15 @@ function startCoreSyncWatcher(plugin, api, wsListener) {
   return {
     cleanup() {
       wsListener.offRaw();
+
+      if (syncPlugin && origEnable) {
+        syncPlugin.enable = origEnable;
+      }
     },
   };
 }
 
 module.exports = {
   isCoreSyncEnabled,
-  startCoreSyncWatcher,
+  startCoreSyncGuard,
 };
diff --git a/server/plugins/headless-sync/plugin/src/main.js b/server/plugins/headless-sync/plugin/src/main.js
index 6d6957e..04adce0 100644
--- a/server/plugins/headless-sync/plugin/src/main.js
+++ b/server/plugins/headless-sync/plugin/src/main.js
@@ -2,7 +2,7 @@ const { Plugin } = require("obsidian");
 const { HeadlessSyncSettingTab } = require("./settings-tab");
 const { WsListener } = require("./ws-listener");
 const { initSyncStatusBar } = require("./sync-status-bar");
-const { startCoreSyncWatcher } = require("./core-sync-guard");
+const { startCoreSyncGuard } = require("./core-sync-guard");
 const api = require("./api");
 
 class IgnisHeadlessSyncPlugin extends Plugin {
@@ -14,7 +14,7 @@ class IgnisHeadlessSyncPlugin extends Plugin {
 
     this.addSettingTab(new HeadlessSyncSettingTab(this.app, this));
 
-    this._coreSyncWatcher = startCoreSyncWatcher(this, api, this.wsListener);
+    this._coreSyncGuard = startCoreSyncGuard(this, api, this.wsListener);
 
     this.addCommand({
       id: "start-sync",
@@ -53,9 +53,11 @@ class IgnisHeadlessSyncPlugin extends Plugin {
   }
 
   onunload() {
-    if (this._coreSyncWatcher) {
-      this._coreSyncWatcher.cleanup();
-      this._coreSyncWatcher = null;
+    window.__ignisHeadlessSyncActive = false;
+
+    if (this._coreSyncGuard) {
+      this._coreSyncGuard.cleanup();
+      this._coreSyncGuard = null;
     }
 
     if (this._syncStatusBarCleanup) {
diff --git a/server/plugins/headless-sync/sync-manager.js b/server/plugins/headless-sync/sync-manager.js
index 8182283..a89adeb 100644
--- a/server/plugins/headless-sync/sync-manager.js
+++ b/server/plugins/headless-sync/sync-manager.js
@@ -124,12 +124,6 @@ class SyncManager {
       throw new Error(`No sync configuration for vault: ${vaultId}`);
     }
 
-    if (this.isCoreSyncEnabled(state.vaultPath)) {
-      const msg = `Cannot start sync for ${vaultId}: Obsidian Sync core plugin is enabled`;
-      this.ctx.log(msg);
-      throw new Error(msg);
-    }
-
     if (state.status === "running") {
       this.ctx.log(`Sync already running for ${vaultId}`);
       return this.getState(vaultId);
@@ -316,31 +310,11 @@ class SyncManager {
     }
   }
 
-  isCoreSyncEnabled(vaultPath) {
-    try {
-      const configPath = path.join(vaultPath, ".obsidian", "core-plugins.json");
-      const data = fs.readFileSync(configPath, "utf-8");
-      const config = JSON.parse(data);
-      return config.sync === true;
-    } catch {
-      return false;
-    }
-  }
-
   autoStartAll() {
     let started = 0;
-    let skipped = 0;
 
     for (const [vaultId, state] of this.states) {
       if (state.autoStart && state.status === "stopped") {
-        if (this.isCoreSyncEnabled(state.vaultPath)) {
-          this.ctx.log(
-            `Skipping auto-start for ${vaultId}: Obsidian Sync core plugin is enabled`,
-          );
-          skipped++;
-          continue;
-        }
-
         try {
           this.startSync(vaultId);
           started++;
@@ -353,12 +327,6 @@ class SyncManager {
     if (started > 0) {
       this.ctx.log(`Auto-started sync for ${started} vault(s)`);
     }
-
-    if (skipped > 0) {
-      this.ctx.log(
-        `Skipped ${skipped} vault(s) due to Obsidian Sync being enabled`,
-      );
-    }
   }
 
   async shutdown() {
diff --git a/src/shims/fs/index.js b/src/shims/fs/index.js
index 966f411..1e70c89 100644
--- a/src/shims/fs/index.js
+++ b/src/shims/fs/index.js
@@ -7,6 +7,7 @@ import { createFsWatch } from "./watch.js";
 import { createWatcherClient } from "./watcher-client.js";
 import { createFdOps } from "./fd.js";
 import { constants } from "./constants.js";
+import { registerReadTransform, removeReadTransform } from "./read-transforms.js";
 
 const metadataCache = new MetadataCache();
 const contentCache = new ContentCache();
@@ -43,6 +44,8 @@ export const fsShim = {
   _metadataCache: metadataCache,
   _contentCache: contentCache,
   _watcherClient: watcherClient,
+  _registerReadTransform: registerReadTransform,
+  _removeReadTransform: removeReadTransform,
 
   async _init(basePath) {
     const tree = await transport.fetchTree(basePath);
diff --git a/src/shims/fs/promises.js b/src/shims/fs/promises.js
index 8155fb7..3f2dbb3 100644
--- a/src/shims/fs/promises.js
+++ b/src/shims/fs/promises.js
@@ -1,5 +1,6 @@
 import { markLocalOp } from "./echo-guard.js";
 import { isInputCachePath, inputCacheGet } from "./input-cache.js";
+import { applyReadTransform } from "./read-transforms.js";
 
 export function createFsPromises(metadataCache, contentCache, transport) {
   return {
@@ -46,60 +47,52 @@ export function createFsPromises(metadataCache, contentCache, transport) {
 
       const wantText = encoding === "utf8" || encoding === "utf-8";
 
+      let result = null;
+
       // Check input cache for files picked via browser file dialogs.
       if (isInputCachePath(path)) {
-        const inputData = inputCacheGet(path);
-
-        if (inputData !== null) {
-          if (wantText) {
-            return typeof inputData === "string"
-              ? inputData
-              : new TextDecoder().decode(inputData);
-          }
-
-          if (typeof inputData === "string") {
-            return new TextEncoder().encode(inputData);
-          }
-
-          return inputData;
-        }
+        result = inputCacheGet(path);
       }
 
-      const meta = metadataCache.get(path);
-      if (meta && meta.type === "directory") {
-        const e = new Error("EISDIR: illegal operation on a directory, read");
-        e.code = "EISDIR";
-        throw e;
-      }
+      if (result === null) {
+        const meta = metadataCache.get(path);
 
-      if (!meta && path) {
-        const e = new Error(
-          `ENOENT: no such file or directory, open '${path}'`,
-        );
-        e.code = "ENOENT";
-        throw e;
-      }
-
-      const cached = contentCache.get(path);
-
-      if (cached !== null) {
-        if (wantText) {
-          return typeof cached === "string"
-            ? cached
-            : new TextDecoder().decode(cached);
+        if (meta && meta.type === "directory") {
+          const e = new Error("EISDIR: illegal operation on a directory, read");
+          e.code = "EISDIR";
+          throw e;
         }
 
-        // binary. ensure we return a proper Uint8Array with .buffer
-        if (typeof cached === "string") {
-          return new TextEncoder().encode(cached);
+        if (!meta && path) {
+          const e = new Error(
+            `ENOENT: no such file or directory, open '${path}'`,
+          );
+          e.code = "ENOENT";
+          throw e;
         }
 
-        return cached;
+        result = contentCache.get(path);
       }
 
-      const data = await transport.readFile(path, encoding);
-      contentCache.set(path, data);
-      return data;
+      if (result === null) {
+        result = await transport.readFile(path, encoding);
+        contentCache.set(path, result);
+      }
+
+      // Apply registered read transforms (e.g., patching synced config files).
+      result = applyReadTransform(path, result);
+
+      if (wantText) {
+        return typeof result === "string"
+          ? result
+          : new TextDecoder().decode(result);
+      }
+
+      if (typeof result === "string") {
+        return new TextEncoder().encode(result);
+      }
+
+      return result;
     },
 
     async writeFile(path, data, encoding) {
diff --git a/src/shims/fs/read-transforms.js b/src/shims/fs/read-transforms.js
new file mode 100644
index 0000000..b462199
--- /dev/null
+++ b/src/shims/fs/read-transforms.js
@@ -0,0 +1,49 @@
+// Post-read transforms for specific file paths.
+// Allows patching file content after reading but before returning to the caller.
+// Used to prevent synced config files from activating conflicting features.
+
+const transforms = new Map();
+
+function normalize(p) {
+  return (p || "")
+    .replace(/\\/g, "/")
+    .replace(/^\/+/, "")
+    .replace(/\/+$/, "");
+}
+
+export function registerReadTransform(path, fn) {
+  transforms.set(normalize(path), fn);
+}
+
+export function removeReadTransform(path) {
+  transforms.delete(normalize(path));
+}
+
+export function applyReadTransform(path, data) {
+  const norm = normalize(path);
+  const fn = transforms.get(norm);
+
+  if (!fn) {
+    return data;
+  }
+
+  try {
+    const result = fn(data);
+
+    if (result !== data) {
+      const before = typeof data === "string" ? data : new TextDecoder().decode(data);
+      const after = typeof result === "string" ? result : new TextDecoder().decode(result);
+      console.log(`[shim:fs] Read transform applied: ${norm}`);
+      console.log(`[shim:fs]   before:`, before);
+      console.log(`[shim:fs]   after:`, after);
+    }
+
+    return result;
+  } catch {
+    return data;
+  }
+}
+
+export function hasReadTransform(path) {
+  return transforms.has(normalize(path));
+}
diff --git a/src/shims/fs/sync.js b/src/shims/fs/sync.js
index e102d3c..59c3f2a 100644
--- a/src/shims/fs/sync.js
+++ b/src/shims/fs/sync.js
@@ -1,5 +1,6 @@
 import { markLocalOp } from "./echo-guard.js";
 import { isInputCachePath, inputCacheGet } from "./input-cache.js";
+import { applyReadTransform } from "./read-transforms.js";
 
 export function createFsSync(metadataCache, contentCache, transport) {
   return {
@@ -58,6 +59,8 @@ export function createFsSync(metadataCache, contentCache, transport) {
         encoding = encoding?.encoding;
       }
 
+      const wantText = encoding === "utf8" || encoding === "utf-8";
+
       const meta = metadataCache.get(path);
       if (meta && meta.type === "directory") {
         const e = new Error("EISDIR: illegal operation on a directory, read");
@@ -65,39 +68,37 @@ export function createFsSync(metadataCache, contentCache, transport) {
         throw e;
       }
 
+      let result = null;
+
       // Check input cache for files picked via browser file dialogs.
-      // These never hit the server; they exist only in browser memory.
       if (isInputCachePath(path)) {
         const inputData = inputCacheGet(path);
 
         if (inputData !== null) {
-          if (encoding === "utf8" || encoding === "utf-8") {
-            return typeof inputData === "string"
-              ? inputData
-              : new TextDecoder().decode(inputData);
-          }
-
-          return inputData;
+          result = inputData;
         }
       }
 
-      const cached = contentCache.get(path);
-      if (cached !== null) {
-        if (encoding === "utf8" || encoding === "utf-8") {
-          return typeof cached === "string"
-            ? cached
-            : new TextDecoder().decode(cached);
-        }
-
-        return cached;
+      if (result === null) {
+        result = contentCache.get(path);
       }
 
-      console.warn("[shim:fs] readFileSync cache miss, using sync XHR:", path);
+      if (result === null) {
+        console.warn("[shim:fs] readFileSync cache miss, using sync XHR:", path);
+        result = transport.readFileSync(path, encoding);
+        contentCache.set(path, result);
+      }
 
-      const data = transport.readFileSync(path, encoding);
-      contentCache.set(path, data);
+      // Apply registered read transforms (e.g., patching synced config files).
+      result = applyReadTransform(path, result);
 
-      return data;
+      if (wantText) {
+        return typeof result === "string"
+          ? result
+          : new TextDecoder().decode(result);
+      }
+
+      return result;
     },
 
     writeFileSync(path, data, encoding) {
diff --git a/src/shims/init.js b/src/shims/init.js
index cca9422..8b5d980 100644
--- a/src/shims/init.js
+++ b/src/shims/init.js
@@ -2,6 +2,7 @@ import { fsShim } from "./fs/index.js";
 import { installRequestUrlShim } from "./request-url.js";
 import { vaultService } from "../services/vault-service.js";
 import { showPluginInstallDialog } from "../ui/bootstrap.js";
+import { registerReadTransform } from "./fs/read-transforms.js";
 
 function resolveVaultId() {
   const urlParams = new URLSearchParams(window.location.search);
@@ -107,11 +108,71 @@ function initPluginPrompt() {
   });
 }
 
+// if headless sync is active, we transform reads of core-plugins.json to hide the sync setting from Obsidian.
+// this prevents headless sync from being disabled as a result of a different device syncing "Active core plugins list".
+// i.e ensure Ignis always has sync: false if headless sync is active.
+// This may be somewhat overengineered. Could revisit later.
+function initCoreSyncGuard() {
+  const vaultId = window.__currentVaultId;
+
+  if (!vaultId) {
+    return;
+  }
+
+  try {
+    const xhr = new XMLHttpRequest();
+
+    xhr.open("GET", "/api/plugins", false);
+    xhr.send();
+
+    if (xhr.status !== 200) {
+      return;
+    }
+
+    const plugins = JSON.parse(xhr.responseText);
+    const headlessSync = plugins.find(
+      (p) => p.id === "headless-sync" && p.bundledPluginId,
+    );
+
+    if (!headlessSync || !headlessSync.enabledVaults.includes(vaultId)) {
+      return;
+    }
+
+    console.log(
+      "[ignis] Headless sync active for this vault, patching core-plugins.json reads",
+    );
+    window.__ignisHeadlessSyncActive = true;
+
+    registerReadTransform(".obsidian/core-plugins.json", (data) => {
+      if (!window.__ignisHeadlessSyncActive) {
+        return data;
+      }
+
+      let text =
+        typeof data === "string" ? data : new TextDecoder().decode(data);
+
+      try {
+        const config = JSON.parse(text);
+
+        if (config.sync === true) {
+          config.sync = false;
+          return JSON.stringify(config);
+        }
+      } catch {}
+
+      return data;
+    });
+  } catch (e) {
+    console.warn("[ignis] Failed to init core sync guard:", e);
+  }
+}
+
 export function initialize() {
   resolveVaultId();
   initVaultConfig();
   initVaultList();
   initMetadataCache();
+  initCoreSyncGuard();
   installRequestUrlShim();
   initPluginPrompt();
 }