End notes are just unbelievably problematic.
But if you only have three, yes, by all means, re-doing them in ID is the way to go. Copy the note text. Delete the note and make sure you get all of the text reference — delete a whole little section of text and retype the end of the sentence to make sure. Insert new note, paste the note text. Repeat for the other two.
Validation is largely an artifact of the "build it from scraps" era of EPUB creation, when it was likely/possible to make many mistakes in the structure of the document. Exporting from tools like InDesign all but eliminates those errors, leaving only a small class of formatting glitches, most of which have zero effect at the reader level. But yes, EPUB distributors can often insist on a perfect validation. Just to make sure, the only validator you should bother with is EPUBcheck. The others either just wrap that same code in their own interface and "improve" it (not), or are outdated or specialized in useless ways. (Or charge for the privilege, something I find obnxious when the core, standard validation code is public-use.)
Sounds like you have it all in hand, once you fix those notes.
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