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Just a guess but do you have an alternate index specified in the Window's advanced properties?
Nope, blank there.
As a test (I do have the originals backed up!) I have emptied the rhkkeyword.apj file and the .hhk file as well. The index of course no longer shows in the .chm, but the same subset of topics show on the Index tab in RH.
Do you use "see also" keywords? If so, are these the ones appearing?
Nope... just standard keywords.
I can see the merged hhk during the build process, and it seems to have the complete list of keywords in it. They also come up if I do a report.
Just a thought--if I create a new project and import all the existing topics, would RH then do a clean recreation of the .apj from the keywords attached to those topics?
Or is the rhkkeyword.apj even involved when the keywords are in the html topic files?
Monday morning update: Friday afternoon the reimporting of topics seemed to be rebuilding the index. This morning, upon reopening the project and resuming the process, the topics I was importing stopped registering on the index tab. Attempting to add them manually, though, resulted in the "topic already exists" message.
Further testing: I added several hundred topics Friday, nothing shows in the rhkkeyword.apj file. All of a sudden today RH is adding index entries there.
This is getting silly.