Keep losing my book progress

[KoGs]

I typically upload my books using Calibre but for certain books I get off kobobooks I need to use Kobo Desktop (well, at least I don't know how else to do it). I never connect my kobo wirelessly or wired unless I have to add books.

So I have this book that I got off kobobooks and uploaded via kobodesktop. I'm at about 50% of it read now. Every time I sync up my kobo the book remains in my "I'm reading" list but the progress goes back to 0% as if I just opened or added the book. Any help?

Thanks.

I should mention I have the original kobo wifi, not touch.