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I'd suggest in this sort of case you start Sigil immediately after you cold boot your computer, in case some other software is doing something interesting. Unplug your network cable (or turn off your wi-fi) and turn off your antivirus.
Epubs in other computers are not any trouble at all, at least for what you are doing. This is what all the talk in the forums of valid epub, something the developers have spent a gigantic amount of time on.
Others may complain that their epubs have been modified from what they put in, but they ARE valid.
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