OK, here's one for your thinking hat.
I've added Missing Recipes mod to my Main game via pasting its content into the Main folder (and of course there's a warning that the main folder's been altered, no multiplayer for you, blah blah blah - don't care) because I already had a game in progress and didn't feel like restarting.
The "missing recipes" mod works - that is, missing recipes have been added.
Now, I want to add this lovely skillbooks mod on top of it. Is there any way to merge it in? If I just paste the RootTemplates folder into Main\Public it doesn't work of course.
Help appreciated!
I won't guarantee anything.

But I've done that, adding Skillbooks to my existing mod and it worked fine on the fly without a restart.