you edit the xml you find beside the nebula's vst .dll file.
in that xml you add entries under the 'datapath' entry that tells nebula where to look. you leave the 'datapath' one alone, but you add others called, i think, 'alternatedatapath'.
you can add one for as many different folders as you like.
i'm kind of too tired right now to go grab my file and actually put an exact example here. maybe someone else will. seriously thought, i just don't feel like it's a good idea to have bazillions of n2p/n2v files from everywhere all in the same big folder.
I used to have separate folders for my Nebula files too, it also enabled me to have specific instances that load much quicker. But I have since put them all back into the same folders and use Zabukowski's Nebula Set-ups program to set up my many specified Nebula instances. Best of all possibilities, in my opinion. Since doing that, I don't see any benefit to having all of the different folders to separate the n2p and n2v files.
Older projects still loaded, just slower than whole projects that have the new dll's. What DID "break" my projects was what I did before using the Nebula Set-ups....(I created separate nebulatemprepository folders and new dll's. Bad idea.....) But everything works great!