EPUB Merge seems to run in background (Worker process?)
I just tested a 3 book merge on 3.1 (w10)
I filled in the metadata.
Then I got a message that it would complete in background BEFORE it would appear (as a format) in the library.
Then I got the confirmation, and it was there

did you start another process before completion (the confirmations might have submerged, not allowing confirmation)
If something was blocking 'workers', I would expect other things would also fail.