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The issue seems to be that there is no program that handles everything to produce an epub and print version.
Seems like the only way to maintain version control is to make sure you keep the same file names in both versions and always work on one after the other.
Of course, if you just are producing an epub, fix it up in Sigil once it is out of InDesign and do all further edits in Sigil. It is quite capable and powerful for epubs and designed for the job.
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