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Like Harvey I welcome you to the forum but please note the cross posting rule. It just wastes time when others are seeking the answer to the same question and leads to different answers in different posts. Messy.
Check out what Harvey has suggested and then post back if no progress.
I haven't worked with HTML help files for some years. Have you tried importing the html topics into a new WebHelp project?
If "Previously on RH3, this manual would normally take 20-30 minutes to load, about 15-30 seconds to refresh while saving changes made when working, and about 40-50 minutes to publish," why did you never split the project into merged help?
See Peter's merged WebHelp tutorial, or use the RH help if you'll need merged .chm output.
When you eventually cease smashing your head against that concrete wall, it feels soooooooo good!