Well, to clear the history, do following:
1. Exit from AllMyNotes Organizer
2. Using Notepad, or any other text editor, open [b]file named allmynotes.cnfg[/b]* in Documents/AllMyNotes folder, and delete text lines from RecentlyOpenedFile0 to RecentlyOpenedFile15.

*For older versions of AllMyNotes file name can be allmynotes.ini.

Is there some way to remove selected files from the selection open [Files > Recent Files], or even just clear the whole buffer that contains the history??