diff --git a/src/brainy.ts b/src/brainy.ts
index 10b30d10..cb1b5fa3 100644
--- a/src/brainy.ts
+++ b/src/brainy.ts
@@ -2308,15 +2308,21 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       // Update storage currentBranch
       (this.storage as any).currentBranch = branch
 
-      // Reload from new branch
-      // Clear indexes and reload
+      // v5.3.5 fix: Reload indexes from new branch WITHOUT recreating storage
+      // Previous implementation called init() which recreated storage, losing currentBranch
       this.index = this.setupIndex()
       this.metadataIndex = new (MetadataIndexManager as any)(this.storage)
+      await this.metadataIndex.init()
       this.graphIndex = new GraphAdjacencyIndex(this.storage)
 
-      // Re-initialize
-      this.initialized = false
-      await this.init()
+      // Rebuild indexes from new branch data
+      await this.rebuildIndexesIfNeeded()
+
+      // Re-initialize VFS for new branch
+      if (this._vfs) {
+        this._vfs = new VirtualFileSystem(this)
+        await this._vfs.init()
+      }
     })
   }
 
diff --git a/src/storage/adapters/fileSystemStorage.ts b/src/storage/adapters/fileSystemStorage.ts
index c7c0dcd1..fb1cfb7a 100644
--- a/src/storage/adapters/fileSystemStorage.ts
+++ b/src/storage/adapters/fileSystemStorage.ts
@@ -870,7 +870,10 @@ export class FileSystemStorage extends BaseStorage {
 
       for (const entry of entries) {
         if (entry.isFile()) {
-          // Handle both .json and .json.gz files
+          // v5.3.5: Handle multiple compression formats for broad compatibility
+          // - .json.gz: Standard entity/metadata files (JSON compressed)
+          // - .gz: COW files (refs, blobs, commits - raw compressed)
+          // - .json: Uncompressed JSON files
           if (entry.name.endsWith('.json.gz')) {
             // Strip .gz extension and add the .json path
             const normalizedName = entry.name.slice(0, -3) // Remove .gz
@@ -879,6 +882,15 @@ export class FileSystemStorage extends BaseStorage {
               paths.push(normalizedPath)
               seen.add(normalizedPath)
             }
+          } else if (entry.name.endsWith('.gz')) {
+            // v5.3.5 fix: COW files stored as .gz (not .json.gz)
+            // Strip .gz extension and return path
+            const normalizedName = entry.name.slice(0, -3) // Remove .gz
+            const normalizedPath = path.join(prefix, normalizedName)
+            if (!seen.has(normalizedPath)) {
+              paths.push(normalizedPath)
+              seen.add(normalizedPath)
+            }
           } else if (entry.name.endsWith('.json')) {
             const filePath = path.join(prefix, entry.name)
             if (!seen.has(filePath)) {
@@ -887,7 +899,8 @@ export class FileSystemStorage extends BaseStorage {
             }
           }
         } else if (entry.isDirectory()) {
-          const subdirPaths = await this.listObjectsUnderPath(path.join(prefix, entry.name))
+          const subpath = path.join(prefix, entry.name)
+          const subdirPaths = await this.listObjectsUnderPath(subpath)
           paths.push(...subdirPaths)
         }
       }
diff --git a/src/storage/baseStorage.ts b/src/storage/baseStorage.ts
index 12da72f0..3b64e9b8 100644
--- a/src/storage/baseStorage.ts
+++ b/src/storage/baseStorage.ts
@@ -279,10 +279,22 @@ export abstract class BaseStorage extends BaseStorageAdapter {
 
       list: async (prefix: string): Promise<string[]> => {
         try {
-          const paths = await this.listObjectsUnderPath(`_cow/${prefix}`)
+          // v5.3.5 fix: Handle file prefixes, not just directory paths
+          // Refs are stored as files like: _cow/ref:refs/heads/main
+          // So list('ref:') should find all files starting with '_cow/ref:'
+
+          // List the _cow directory and filter by prefix
+          const allPaths = await this.listObjectsUnderPath('_cow/')
+          const filteredPaths = allPaths.filter(p => {
+            // Remove _cow/ prefix to get the key
+            const key = p.replace(/^_cow\//, '')
+            return key.startsWith(prefix)
+          })
+
           // Remove _cow/ prefix and return relative keys
-          return paths.map(p => p.replace(/^_cow\//, ''))
-        } catch (error) {
+          return filteredPaths.map(p => p.replace(/^_cow\//, ''))
+        } catch (error: any) {
+          // If _cow directory doesn't exist yet, return empty array
           return []
         }
       }