Try the original CL "Always persist bookmark IDs" again with the fix to...

chrome/browser/gtk/bookmark_tree_model.h

Index: chrome/browser/gtk/bookmark_tree_model.h
===================================================================
--- chrome/browser/gtk/bookmark_tree_model.h	(revision 20552)
+++ chrome/browser/gtk/bookmark_tree_model.h	(working copy)
@@ -6,6 +6,7 @@
 #define CHROME_BROWSER_GTK_BOOKMARK_TREE_MODEL_H_
 
 #include <string>
+#include "base/basictypes.h"
 
 class BookmarkModel;
 class BookmarkNode;
@@ -36,12 +37,12 @@
 // |recursive| indicates whether to recurse into sub-directories (if false,
 // the tree store will effectively be a list). |only_folders| indicates whether
 // to include bookmarks in the tree, or to only show folders.
-void AddToTreeStore(BookmarkModel* model, int selected_id,
+void AddToTreeStore(BookmarkModel* model, int64 selected_id,
                     GtkTreeStore* store, GtkTreeIter* selected_iter);
 
 // As above, but inserts just the tree rooted at |node| as a child of |parent|.
 // If |parent| is NULL, add it at the top level.
-void AddToTreeStoreAt(const BookmarkNode* node, int selected_id,
+void AddToTreeStoreAt(const BookmarkNode* node, int64 selected_id,
                       GtkTreeStore* store, GtkTreeIter* selected_iter,
                       GtkTreeIter* parent);
 
@@ -53,7 +54,7 @@
     GtkTreeIter* selected);
 
 // Returns the id field of the row pointed to by |iter|.
-int GetIdFromTreeIter(GtkTreeModel* model, GtkTreeIter* iter);
+int64 GetIdFromTreeIter(GtkTreeModel* model, GtkTreeIter* iter);
 
 // Returns the title field of the row pointed to by |iter|.
 std::wstring GetTitleFromTreeIter(GtkTreeModel* model, GtkTreeIter* iter);