DisturbedDragon, back in June this year we had
a problem with FFF reporting "Not a Zip File" but it only happened with email update and Smarten Punctuation and has since been fixed.
When exactly are you getting that error? While trying to download? FFF shouldn't be wrecking the existing epub if it has a problem. If you can reproduce the problem, please run Calibre in debug mode and post the debug log.