diff --git a/apps/desktop/src/app/chat/sidebar/index.tsx b/apps/desktop/src/app/chat/sidebar/index.tsx
index d3dd287ba5..fcc84966c8 100644
--- a/apps/desktop/src/app/chat/sidebar/index.tsx
+++ b/apps/desktop/src/app/chat/sidebar/index.tsx
@@ -1008,7 +1008,15 @@ export function ChatSidebar({
     // Layer the user's manual drag-order on top of the deterministic sort. Empty
     // (default) returns `sorted` untouched; projects the user hasn't ordered yet
     // keep their sorted position rather than jumping the hand-picked list.
-    return orderProjectsByIds(sorted, projectOrderIds)
+    // Deduplicate by id — safety net for backend merge edge cases
+    // (e.g. Windows path-casing differences across profiles).
+    const seen = new Set<string>()
+    const deduped = sorted.filter(project => {
+      if (seen.has(project.id)) return false
+      seen.add(project.id)
+      return true
+    })
+    return orderProjectsByIds(deduped, projectOrderIds)
   }, [
     projectTree,
     dismissedAutoProjects,
diff --git a/hermes_cli/web_routers/profiles.py b/hermes_cli/web_routers/profiles.py
index aa1c3487a4..9672eb29ec 100644
--- a/hermes_cli/web_routers/profiles.py
+++ b/hermes_cli/web_routers/profiles.py
@@ -16,6 +16,7 @@ from hermes_cli.web_read_coalescing import coalesced_read
 import inspect
 import json
 import logging
+import os
 import re
 import subprocess
 import sys
@@ -687,7 +688,7 @@ def _merge_profile_tree(
             session["profile"] = profile
             session["is_default_profile"] = profile == "default"
 
-        key = project.get("path") or project["id"]
+        key = os.path.normcase(project.get("path") or project["id"])
         existing = merged.get(key)
         if existing is None:
             merged[key] = project