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Jon - I think its the same issue as Find Duplicates exemptions, have a look in the database preferences opf file and you may find some book numbers listed pertinent to your RL.
Kiwidude devised a means to persist the Marks some of his plugins created. Remember the plugins were written well before Marks were shown in the book list as Frat Pins, and he'd already 'retired' when that happened.
I'm not sure about RLs usage of persistent Marks, but I know that FD's exemptions have their Marks re-established when a library is opened. RL probably does the same.
BR
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