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Welcome to the forum.
I would certainly make a copy of the whole shebang (all projects) and make the tags and expressions identical. I don't know precisely how the conditionals are applied, but it seems logical that the topic-level tags and the text-level tags would be processed separately and might give different results.
Let us know what happens -
I did make all build expressions in the sub-projects identical to those in the master project, but that didn't fix the problem. Another problem is the master project has about 5 more build tags than the sub-projects to accommodate different deliverable needs. So, since those tags weren't created and defined in the sub-projects, they aren't available when creating the expression definition. Do you think that is causing a problem?
I think I'm the one causing the problem - I don't think I read your initial post carefully enough. Sorry...
I can't figure out how this is happening. When you merge .chms, you have already compiled the 'slave' projects. The link from the master TOC points to a slave .chm - which you say is working correctly when opened on its own.
Since the slaves and masters are compiled independently, there shouldn't be any interaction between the master and slave build expressions - and if there is one, it should be excluding more topics, not including more topics!
The typical problems people have with merged .chms seem to be TOC issues (does the master TOC show up, or just the slave project's TOC?) and path issues (the master can't find the slaves). However, I did see one or two posts on this forum where the master was pointing to old copies of the slave .chm - could you have a "complete" .chm lurking about?
BTW, according to RH help, binary indexes are fine in merged HTMLhelp. Binary TOCs are not. I don't think you have this problem, because the symptoms are different, but you could take a look - the setting is in the HTMLHelp Generate wizard. Click the [Advanced] button on the first wizard page and look on the TOC tab to make sure Binary TOC is not checked.
You might also do a quick search on the General Info/HTMLHelp/RH for HTML forums for "merged .chm" - you might recognize a symptom in someone's post that I didn't catch.