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This is (almost) invariably caused by a mix of fonts installed on the system., for Macs in particular. Something about how fonts are managed both by the system and CC/InDesign... and there my understanding of it runs out.
If you're on Windows, uninstall or deactivate the whole font family and then do a clean reinstall from a 'best' source like Adobe or Google if you don't have original, uncorrupted font files from some other source.
Making sure the system has one and one only set of that font is usually enough. But you might need to do the IDML to INDD save/purge step after the fonts are cleaned up, as well.
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I found 1 additional instance of the font and deleted it, but the problem remains. I have discovered that a PDF of the whole book does not have this issue, nor do ePUB exports of individual chapters - it seems to be tied to exporting the whole book to an ePUB. On a critical deadline, hoping someone has previously dealt with this issue.
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This is not an uncommon problem. It comes up a few times a year here. I can't think of a time that it didn't trace back to a font "mapping" issue caused by one system/app fault or another. I also can't think of a time that the specific, technical fault was ever isolated; fixed EPUB is such a mess that you can only keep changing the input components and hope it straightens out.
But deleting one stray font isn't the solution, nor quite what I suggested. 🙂
First, try substituting any similar font — mostly, of approximately the same style and width. While the layout and the export might be a bit messed up, I'd bet that will elimatie this erratic mapping. (Unless you choose a second font with the same problems...)
Then, delete the ENTIRE faulty font set from your system. Uninstall, deactvate, remove font files. Nothing short of that has ever seemed to fix either corrupted font files or faulty "mapping" of the fonts as ID uses them. If you're on Mac, be sure you clean out all the various font repositories. (Again, I understand that ID and/or Adobe maintians one separate from the system cache... but that's the limit of my understanding.)
Then, install the font from new, clean files, from an original source if possible, not through a font website.
And it's probably a good idea to do the save to IDML and reopen/save as new INDD purge to clear any remaining corruption or faulty font assignments.
If ALL of that doesn't solve the problem, it's going to be a tougher fix. To the best of my recollection, though, these steps have fixed this exactly export problem multiple times before.
The real solution, overall, being... don't use fixed-page EPUB. 🙂
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Unfortunately, I don't have the option of a reflowable ePUB and am on a deadline. It's a 920-page book, so also not an option to change any fonts at this point. Will try the IDML suggestion, thank you.
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I assumed the project was FXL for Good Reasons. My comment was meant for the future — talk bosses and clients out of using fixed-layout EPUB whenever possible. It seems like the simple, obvious choice, especially to anyone not familiar with the nuts and bolts of digitial publishing, but it's a poor choice in nearly every respect. (If you want EPUB/e-book, use reflowable. If you want digital page representations, use PDF. There is no good third option.)
Suggestion to swap fonts was a test, not a solution. If a clone font fixes the problem, it nails it as a font-mapping issue. Fix the underlying font problem, and the export problem should go away.
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Having been in these very shoes myself, on a client's Mac, having not touched a Mac since before 2020, let me say that you are going to be best served here by spending some time cooking up variants on the search string "clean Mac font cache". Adobe has some instructions posted, but if you have any Extensis products installed, you're going to want to look at their font cache cleaning instructions as well. Any other font tools installed? Be really thorough.
My client had an app installed that was, I think, exclusively meant for cleaning one's font caches on a Mac, and the way we got the epub to export successfully was to use all three (app, Extensis instructions, Adobe instructions, I think in that order).
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I wouldn't mind working this through (this time or some future event) with someone who knows the nuts and bolts, so that I can document it a little more thoroughly and with less helpless handwaving. 🙂
( So I'm a Windahs guy. Like, y'know, sue me. 😄 )
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Was that really necessary? Come on.
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It's funny to those of us who go home with a migraine at the very mention of "PC vs Mac." But I'll avoid humor in all subsequent posts.