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TOC problem when tags pulled include sub or superscript. After the sub or superscript the link is dead. Any way to fix this other than manually copying the hypertext after the sub/super?
It looks like you've already found one suggestion - use natively sub/supscripted glyphs if your Unicode font populates them, and don't use Character Formats to accomplish it.
Another sort-of fix is to delete the offending formats from the Character Catalog in the TOC file. The generated text strings won't contain any sub/sups, but the PDF links will work.