What a mess. Deleting and then pasting back in the offending text did nothing. Saving as idml did work except a different piece of text that is a dead link to a website now surfaces. And I lost the links to my (few) footnotes. Time to take a break.
Just went back to my original. Everything works but I get messages in Quality Check that the footnotes are not backlinked. But they are working.
Did this book originate in Word, and then import to ID? That's another whole chain of possible faults.
When you replace the footnotes, or any time you do that kind of step, it's critical to make sure you delete everything that could contain a bad link. If, for example, you have a footnote at the end of a paragraph, cut ALL the text of about the last sentence in the first para and the first one in the second and delete it from the document. That should remove the footnote, the reference any any stray bits of a broken or orphaned link.
THEN paste the text back in using a "plain text" option; the best trick might be to paste it into Notepad, then cut and paste it from there. That keeps old 'crud' from getting pasted back in.
THEN insert a new footnote and paste similarly clean text into it.
A lot of steps but it does little good to cut and paste a broken or orphaned link back into the doc.