I had that happen with a sideloaded book as well. But when I'd go to the home screen it said I was on page "1 of 1." This is a book with 700 pages. When I'd reopen it, I'd get that "sync to furthest location?" dialogue that would take me from page 1 to wherever I'd been reading it before.
But I did an epub-to-epub conversion in Calibre and it fixed that.
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