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I assume you mean greyed out in Finder, which means it's probably a MacOS/HFS+ issue rather than a calibre issue. A search for "why are some files greyed out in finder" may provide some answers.
What tool(s) do you use to do the backup/restore.
Maybe MacOS regards .db files as something 'special'. I've had Windows tell me that they were 'system' files, although it didn't prevent me doing what i wanted.
BR
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