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If I delete a table, the file size stays the same as the maximum size the file reached. Is there a query I can run or a feature I'm missing to be able to shrink the file size of the db?

I'm not sure how SQLite Administrator manages it but see http://www.sqlite.org/lang_vacuum.html for the standard SQLite command.

Regards,

Ben

yes, the "clean up database" menu item does the vacuum command for you