Hopefully Peter will pop in with better advice as it relates to merging.
Content Categories is an interesting feature, but it does exponentially create a new swarm of files for each category you create. Basically, each Category constitutes a new WebHelp output. If you have more than one category, pay close attention to the dialogs you see as you generate the output. You will notice a "Generating (Category name)" for each category.
I am not certain that Content Categories will work with merged help. Certainly I would not be testing it with your live setup. Download the merged help demo from my site and experiment with that. It's more basic and easier to see what is going on. I will try to have a look but it will not be until later tomorrow at best. A distant bell is telling me that I was advised it will not work but I would want to test and also check that before being definitive.
I have been told that Dynamic Content Filtering in Responsive HTML5 layouts will work across a merge as long as the filtering is set up in the same way and using the same names. Unless there was some reason not to, that is what I would be looking at.
Post back tomorrow to let us know if you have made any progress. If not, then I will take a look as soon as I can.
See www.grainge.org for RoboHelp and Authoring information
I tested with the sample project. I'll have to work through some kinks, like linking between content categories, but I think it may work. Thanks for weighing in!