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If some file paths aren't being correctly updated when opening an epub, it usually means their paths in the original opf manifest weren't correct to begin with. Sigil's automatic link updating routines require the paths in the opf to be correct.
Are you saying every path except the ones to .png files are being correctly updated?
Also, what version of Sigil are you using? I believe there were changes made to more recent versions so that duplicate file names (in different folders) could be accommodated.
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