Hi theDucks,
Sigil always flattens the structure on input. That said, I have tried to make changes to Sigil in master to work around this and properly come up with unique names for each file without hurting anything but the layout. I will talk to user-none about some sort of warning when it occurs.
If you could post a link to an epub that you know Sigil currently messes up when flattening, I would love to have it to test and fix Sigil master with so that this entire problem goes away when Sigil 0.9.0 is actually released.
Thanks,
Kevin
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