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You might try going into the !SSL! folder and deleting the chw file as well as the old chm files you *don't* want to be merged. My experience is only with RH5 so if RH 6 handles merge differently, my advice may not be correct.
Well, that's really weird. After deleteing all chm files in the project root directory and recompiling, the merged TOC isn't occurring any more, although the incorrect merge files are still listed in the hhp file. I've deleted them several times, and RH keeps adding them back.
If anyone can throw light on where these references come from I'd be grateful, as I need to set up the merge again, but the correct file references are being replaced by the old incorrect ones.
Oh, further information, the project is in Visual Source Safe. Maybe that is the problem, as when I try to recreate the merge references in the TOC I get the following error "The files in the list below could not be found in version control. You may need to get the latest version of this project before you can execute the selected action".
(Of course it isn't in source control! I deleted the references, and RH obligingly deleted it from VSS for me!!! and not to mention is shouldn't be in source control here, but that's another story entirely...)
Okay, I finally found the answer.
In the xpj file, there is an xml tag section starting "mergedhelpfiles". The list of files here is used to generate the [MERGE FILES] section of the hhp file. This list didn't correspond with the list of linked CHM files in my table of contents.
So I manually edited the files and now the correct list of files is being placed in the HHP file.