Not sure if this will help but it did for me when I had a similar problem (it has been a while since I've used this set up but I'm assuming it will still work). You can set calibre to add a specific tag to books when they are added to the library - I had mine set as @added. Then using the tags browser you can find all @added books and do a bulk metadata change (ie. clear all tags etc). It takes very little time if you're adding books in bulk - it would be of little use if you're adding a single book here and there though.
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