Autotag breaks internal cross-references

I'm working on a document composed entirely of enumerated sections, paragraphs, and subparagraphs, and many cross-references (100+, I'm sure). The cross-references have a character style applied to them. I then mapped styles to tags, which caused all the cross-references to break and no longer have a destination. At that moment, I didn't make this association, so I just relinked the cross-references manually. I went on to make some further adjustments to the layout, adding a few subparagraphs and converting some that were mistakenly styled as paragraphs to subparagraphs. After autotagging, all the cross-references again lost their destinations. ALL of them (not just the ones from new paragraphs or re-styled paragraphs). Does anyone know why this is happening, or how to prevent it?