So, it seems not all clients are putting default bookmarks on the same note kind...
Clients should be saving bookmarks to your standard kind 10003 list. However, there are a lot of clients that use other event kinds, such as the deprecated kind 30001.
You can use listr.lol to manage your various bookmark lists. Once you can identify which one is your kind 10003 (Mine was titled "Bookmarks") you can add the content from your other "bookmark" lists that are likely kind 30001 lists.