InDesign 14.0.1 x64

I have an 1100 page document that is primarily legal code and guidance, with several hundred cross-references to text anchors. The idea being that you can jump around easily in the document to get info on referenced code information.

When I export to an interactive PDF, not all of the links work. I'm not able to predict which links will and won't work before export, but once exported those links will.not.work. When I check the PDF link info, the correct link information is there, it simply doesn't work. I can edit the link by manually selecting it and reconnecting it to the place it's (ostensibly) already connected, and it will work fine.

However, with several hundred cross-references, this is NOT a tenable solution.

Exporting the document as individual pages does not fix the problem.
Exporting in chunks does not solve the problem.
Exporting as an ePub also doesn't solve the problem.

I can convert the file to an IDML file, reopen it, then export, and at that point all of the links will work...

HOWEVER:

Reopening after conversion shows a MESS of formatting errors that are unpredictable. In one instance, a number of carriage returns were randomly preceded by a soft return, which was reasonably fixable. In another instance, however, bulleted paragraphs had their formatting tags shifted by one paragraph up or down. Which necessitates going through 1100 pages of legal code and associated text and double checking every single instance of a bullet or numbering - i.e., multiple instances, every page. Which is also NOT a tenable solution.