Calibre is wrong about which versions of a book are on my device

I recently imported one of my back-up libraries into Calibre, which might have caused this problem? Because now there are duplicates of many books in my Calibre library (usually just two versions total).

And Calibre is incorrect about which ones are on my Kobo. It claims the AZW3 versions are on my Kobo, which is obviously not the case. (I did triple-check, but no, all the files on the Kobo are EPUB, just like they should be.)(Specifically EPUB, not KEPUB, in case that's relevant.)

The versions of the books-on-Kobo are still in Calibre, they haven't been removed or the metadata edited or anything. I don't know why Calibre's not recognising that these are the books on the device.

Is there any way to make Calibre (or the Kobo) do some kind of sync to correct this? (I did try the 'update cache metadata on device', but that didn't help.) Currently the Kobo isn't displaying things like the correct series metadata because that information isn't attached to the versions of the books it thinks (or Calibre thinks?) are on there.

I don't know the right terminology for any of this so I hope this makes sense to those better-versed than me!