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Sigil is an EPUB2 editor, but that doesn't prevent people from editing EPUB3 files, which end up with broken OPF when you save them.
Sigil development seems to have stalled, the last year has primarily seen bug fixes instead of development of new features and there seems no active development to support the latest version of the EPUB standard after the an assessment made in 2013.
Should I look for another editor that at least doesn't break my EPUB 3 files, even if not supporting all EPUB 3.0 features?
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(2)More posts by @Lorraine
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Personally, I stay away from Sigil and Calibre precisely because they break files and don't show you exactly what they're doing—unless a tool lets me modify all the navigational files directly, I'm not going to trust that it's doing things correctly. I use Notepad++ or Geany for epub editing. If you must use an editor, try the Blue Griffon Epub Edition or the Oxygen XML Editor; they're much more powerful tools.
So, to answer the question "what can I do about Sigil breaking epub 3 files": Don't use Sigil.
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There is some hope on the horizon for the many users of EPUB3 files¹
masayoshi takahashi has presented a relatively small pull request with changes for the Sigil source base that does prevent Sigil from breaking the OPF file when saving EPUB 3.
Hopefully the next Sigil release will incorporate these. In the mean time you can of course compile your own Sigil to include these changes, try them out and report any issues if you encounter them.
¹ The style-sheet facilitates in EPUB 3 support the top-bottom written languages, most Japanese EPUB Ebooks are EPUB 3
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