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With the recent changes in InDesign, now the EPUB 2 ebooks are not valid anymore. There are at least two problems.
First, the xml:lang attribute in content.opf file is not allowed in package element on EPUB 2 ebooks. This is ok in EPUB 3 ebooks.
Second problem is about ebooks with footnotes. The recent change how InDesign exports footnotes is not a valid way for EPUB 2 ebooks.
I'm happy to see that you develop the accessibility side in InDesign so users can create more accessible EPUB 3 ebooks but I hope you would test your new features in EPUB 2 ebooks as well. Just create an EPUB 2 ebook and run it through epubcheck 5.1.0 and you will see these errors.
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Well, you can probably anticipate the answers here.
First, EPUB2 is a very old format, 15 years since its prime. For many reasons, it's overdue to switch new projects to EPUB3 (which is not a lot newer, but at least has been updated since 2011).
The other part of the answer is that accessibility as a more general and supported feature is long overdue, so it's either work with it or try to cling to outdated versions of EPUB etc. to preserve your workflows.
Why are you still exporting to EPUB2?
What problems, exactly, are you seeing with the accessibility changes?
I think that regardless of the answers, the one and only solution is that it's well past time to update your layout, export and production workflows. Don't overlook the lengthy Accessibility control panel under Metadata; you might be able to disable or tweak the export changes that are causing problems. (That wouldn't be my first choice, for several reasons.) But if you revisit your layout and export model, you can probably get around the changes... and maybe even preserve export to EPUB2, although I'd again suggest it's a decade past any justification for not making the jump to the updated standard.