Tim,
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.
Harvey