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I also have a large collection of books which stalled at 80% during Kobo Processing of the entire collection.

I discovered via Sigil and Calibre that several books had major errors in their TOC and structural errors in the code, I first cleaned them in Sigil, then fixed the TOC in Calibre and bug checked in calibre.

With a large unverified collection I would batch load the books.
Whenever I do a clean install of my entire collection to my Glo I batch load then, 200 per batch, let the Glo process 200 at a time and it works fine.