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Sorry, Peter, I didn't see you there, in between me and me. I'm deleting this me.
You say you entered the keywords again but you don't say you recreated the links. I wonder if you thought adding the words again would automatically do that?
When you regenerate the help, trying doing so to a new folder and see if the index still behaves correctly.
It sounds like you imported some topics from one project into the other. Is that correct?
If so, the updated project has no record of the new keywords, even though a topic may bring in an information tag about being indexed. After you insert the new keywords, the project has no record of any links for them until you re-index the affected topics.
I can't recall whether X 5.0.2 has an "Import index" function. If it does, that's the best way. You need not delete the new, unlinked entries.
If you changed filenames or topic titles, the old links may not carry over.
If you combined topics by copy-and-paste, the above might work if the "from" and "to" topics have the same filenames and titles.
Otherwise, you need to run the indexer again, just on the affected topics.
And could it be the keywords are held in the topics rather than the HHK file?