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Sigil always relocates the files to suit its own internal structure, but it always updates the links in the various files. Is it only in iBooks that the links in the toc don't work?
Do you have a small uncopyrighted sample that you can post that will show broken links in the ToC when following your steps? So far none of my tocs have broken links when I follow your steps. Granted: I don't have iBooks to test with, but if the Epub is valid and has a working toc before opening it in iBooks, then clearly iBooks is doing something weird. For it to be a Sigil bug, there would have to be something broken immediately after the Save As.
For clarity, are you useing Save As, or Save a Copy?
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