Josh -
Yet another idea is to destroy the global flaps, and rerun whatever initialization method(s) created them during the filein process. I don't know how complicated this would be; I've been unable to find out how to do this, either.
Having just visited this region for other reasons (space reclamation), I offer the following suggestion:
1. Use the preferences... window to set useGlobalFlaps to false.
2. Browse to System-Support/Utilities
3. In the class pane choose class vars to inspec the class variables
4. Select the item 'FlapTabs' -- it will show an orderedCollection
5. In the value pane, select all that, replace it by 'nil' (without the quotes), and choose 'save' from the menu or use cmd-s
This should put you in such a condition that, if you then turn the useGlobalFlaps preferences on again, it will recreate things from scratch.
Good luck.
- Dan