Something simular happened to me, yesterday. I sideloaded three books, and I loaded one through Calibre, and ejected before disconnecting.
Processing took ages, so I connected my Kobo Glo again, this time to Kobo desktop, and ejected, but with the same result, ereader kept processing.
I connected a third time and ejected my Kobo Glo safely from my pc (twice, since I have an SDcard in it) and then my ereader finally acted normal.
I didn't do a factory reset.