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Those are not error messages, but a true helpful message.
View Manager and many, but not all, plug-ins keep their preferences that are database-specific (a.k.a. library-specific) in metadata.db table preferences.
CALM is an add-on, not just a plug-in, because it comes with a special template metadata.db that is extracted from the CALM .zip file when you click "refresh".
CALM also has a companion database, metadata_tools.db, which is where your 'permanent' customizations are cached until you need them put back into metadata.db after it has been freshly extracted from the .zip.
Those messages are "good". Always say "yes, please". Otherwise, you will have to re-customize View Manager etc. each time you refresh the Target Library.
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