diff --git a/apps/desktop/src/main/main.ts b/apps/desktop/src/main/main.ts
index a3c24c742..9d6a59a25 100644
--- a/apps/desktop/src/main/main.ts
+++ b/apps/desktop/src/main/main.ts
@@ -78,6 +78,7 @@ import {
 import { inspectRecentProject, type RecentProjectInspection } from "./services/projects/recentProjectSummary";
 import { resolveProjectIcon } from "./services/projects/projectIconResolver";
 import { normalizeStartupProjectState, resolveStartupProject } from "./services/projects/startupProjectResolver";
+import { collectRootsBoundToWindows } from "./services/projects/projectContextRoots";
 import { createAdeProjectService } from "./services/projects/adeProjectService";
 import { createConfigReloadService } from "./services/projects/configReloadService";
 import { IPC } from "../shared/ipc";
@@ -1191,16 +1192,13 @@ app.whenReady().then(async () => {
       }
       : null;
 
-  const rootsBoundToWindows = (): Set<string> => {
-    const roots = new Set<string>();
-    for (const root of windowProjectRoots.values()) {
-      if (root) roots.add(root);
-    }
-    for (const tabRoots of windowProjectTabRoots.values()) {
-      for (const root of tabRoots) roots.add(root);
-    }
-    return roots;
-  };
+  const rootsBoundToWindows = (): Set<string> =>
+    collectRootsBoundToWindows({
+      windowProjectRoots: windowProjectRoots.values(),
+      windowProjectTabRoots: windowProjectTabRoots.values(),
+      windowPendingProjectRoots: windowPendingProjectRoots.values(),
+      projectInitPromises: projectInitPromises.keys(),
+    });
 
   const emitProjectChangedToWindow = (
     windowId: number | null,
diff --git a/apps/desktop/src/main/services/projects/projectContextRoots.test.ts b/apps/desktop/src/main/services/projects/projectContextRoots.test.ts
new file mode 100644
index 000000000..f60c58c03
--- /dev/null
+++ b/apps/desktop/src/main/services/projects/projectContextRoots.test.ts
@@ -0,0 +1,27 @@
+import { describe, expect, it } from "vitest";
+import { collectRootsBoundToWindows } from "./projectContextRoots";
+
+describe("collectRootsBoundToWindows", () => {
+  it("includes pending and in-flight init roots so rebalance cannot evict mid-open", () => {
+    const roots = collectRootsBoundToWindows({
+      windowProjectRoots: ["/old-repo"],
+      windowProjectTabRoots: [new Set(["/old-repo"])],
+      windowPendingProjectRoots: [new Map([["/new-repo", 1]])],
+      projectInitPromises: ["/warming-repo"],
+    });
+
+    expect([...roots].sort()).toEqual(["/new-repo", "/old-repo", "/warming-repo"].sort());
+  });
+
+  it("deduplicates the same root across binding sources", () => {
+    const roots = collectRootsBoundToWindows({
+      windowProjectRoots: ["/repo"],
+      windowProjectTabRoots: [new Set(["/repo"])],
+      windowPendingProjectRoots: [new Map([["/repo", 2]])],
+      projectInitPromises: ["/repo"],
+    });
+
+    expect(roots.size).toBe(1);
+    expect(roots.has("/repo")).toBe(true);
+  });
+});
diff --git a/apps/desktop/src/main/services/projects/projectContextRoots.ts b/apps/desktop/src/main/services/projects/projectContextRoots.ts
new file mode 100644
index 000000000..3adfbfb25
--- /dev/null
+++ b/apps/desktop/src/main/services/projects/projectContextRoots.ts
@@ -0,0 +1,25 @@
+/**
+ * Roots that must be treated as "in use" for project-context retention and rebalance.
+ * Includes window bindings plus in-flight opens (pending IPC authorization and init promises).
+ */
+export function collectRootsBoundToWindows(args: {
+  windowProjectRoots: Iterable<string | null>;
+  windowProjectTabRoots: Iterable<Set<string>>;
+  windowPendingProjectRoots: Iterable<Map<string, number>>;
+  projectInitPromises: Iterable<string>;
+}): Set<string> {
+  const roots = new Set<string>();
+  for (const root of args.windowProjectRoots) {
+    if (root) roots.add(root);
+  }
+  for (const tabRoots of args.windowProjectTabRoots) {
+    for (const root of tabRoots) roots.add(root);
+  }
+  for (const pendingRoots of args.windowPendingProjectRoots) {
+    for (const root of pendingRoots.keys()) roots.add(root);
+  }
+  for (const root of args.projectInitPromises) {
+    roots.add(root);
+  }
+  return roots;
+}