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I actually had something very similar to what was described happen with a couple of stories... except mine was with epub and a nook.
The problem turned out to be caused by improper html in the source of chapter. The nook couldn't handle it, but calibre was able to. Upon opening the epub with Sigil and then saving it would work on the nook and FFDL was able to continue updating without issue.
Not sure if this is what you are experiencing or not, but the epub download with conversion to mobi has been identified a few times as the way to go for mobi format stories
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