Which version of RoboHelp are you using? I ask because in version 9 a feature was added that is called "Content Categories". With Content Categories this should be feasible. You simply create more than one glossary, then define different Content Categories and ensure you point to the specific Glossary you wish to use with the category!
But CC also duplicates the entire content, for the sake of only a glossary. Seems a bit overkill to me.
How about topics with the glossary terms that uses can switch between?
I will look into this option.
I got Robohelp ver 10.