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FYI, Sigil has always done this. It is how it operates. When you load an epub into Sigil, Sigil reformats it to fit its internal layout. Parses all files and reserializes them to make sure their src and href links are properly updated, etc. None of the changes you mention should break anything.
So some questions:
In BV, does your epub function after loading?
Were all the files well-formed when loading?
If not, enable Mend on Open and reopen the epub.
Was this a epub2 or an epub3?
Was this a fixed layout?
If an epub2, please try running the Flightcrew plugin to see if it detects any breakage.
Or you can run epubcheck (via plugin) and again see if any breakage is detected, before writing the epub out.
That should point to anything funny.
Let us know what it reports and we can try to help.
KevinH
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