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Those are not files in the database but references to the deleted files. I would force a rescan of my tags.
To force a Database rescan: Main Menu> Database (Long press on Enter)> Initialize Now. According to the manual:
Initialize Now: You can force Rockbox to rescan your disk for tagged files by using the Initialize Now function in the Database Menu. Warning: Initialize Now removes all database files (removing runtimedb data also) and rebuilds the database from scratch.
Always works for me.
the page in the manual. Glad to hear you are using it. Not what I would choose for light reading
but there's a wealth of carefully thought out information there. Good stuff.