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As far as the OPF is concerned, part of the problem is that paths like "OEBPS/../cover.jpg" passed in the keylist parameter to xmlprocessor.performOPFSourceUpdates() are not matching the ../cover.jpg href in the OPF manifest ... so no updates are performed on those entries (even though the new/correct path is available in the valuelist parameter).
os.path.normpath-ing the keylist entries will allow the match to happen and the OPF file will be properly updated, but that does nothing for the NCX entries, or any of the links in the xhtml, or the xref:link parameter in the SVG cover code. I have a feeling there's a more universal change to be made that will handle the overall situation better that I'm missing.
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