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0e1f616
(Get the code!)
The migration already is handled automatically by Gtk3 and that is the problem. Gtk3 migrated you years ago without you knowing about it. Since then you have had two bookmark files with different contents. The only effect you would see is that file requesters would show different bookmarks to thunar.
There is nothing Xfce can do about this because we have no way of knowing which one you want to delete and which one you want to keep, in order to bring them in sync.