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I haven't worked on any projects that require index entries in quite a while, so I don't remember if I've ever had this problem. One thing you haven't mentioned trying is exporting to IDML and opening the resulting file to see if the problem is still there. Maybe worth a try.
Thank you for your idea. I exported it as an IDML and opened the resulting file and the problem is still there. As I'm adding index entries, it seems rather hit and miss as to whether or not the markers appear in the Story Editor. (Just added two on the same topic and both are "invisible:
When .idml doesn't fix things I usually export the story to InDesign Tagged Text and either wipe out the orignal, frames and all, and place the tagged text in the same file, or place it into an entirely new document to be sure I'm not preserving any corruption.