I think you already added your own fix, but just in case it helps, I think I figured out a solution earlier.
I changed every tenth registry key to be a single digit (20 becomes 3, 30 becomes 4, etc). This prevents any individual policies from the initial release from leaving orphaned registry keys that could cause issues, while also maintaining the order in both the group policy editor and Windows registry (1, 12, 13, 14, ..., 19, 2, 21, 22, ..., 28, 29, 3, 31, etc) which ensures a folder with lots of bookmarks remains in the expected order.