Something has drastically changed with importing multiple OBJ files into Zbrush now with 3.5. 3.5R3 to be specific.
Used to be you could click on that little star looking thing and then import an OBJ file and thus assemble a model in Zbrush 3.1 by appending the parts to a main part, and your OBJ files would all load in the proper position and size relative to each mesh’s position and size from your export program.
Now I can’t seem to be able to load more than one OBJ file at a time. If I try to import a new one it simply replaces the one that had been loaded.
Is there something I’m overlooking here or is this an intentional limitation for some reason?
Thanks. 
No replies at all? :lol:
I figured it out anyway. You have to load a new polymesh for each new OBJ file you want to import. So you could clone your polysphere many times to have versions of it available, since you lose it with each new OBJ import, or you could load a sphere3D each time, then convert it to a polymesh.
I would really like to see Zbrush soon have a more normal and typical way of importing obj files.
This used to happen to me as well in 3.1. What I do is create one subtool, when I successfully append a 2nd subtool. I save out and reload. If I persisted in add subtools the first would disappear to replaced by the newest one imported. So for each successfully appended subtool, save out and reload the subtool. It’s a pain, but I find it works for me 
I usually just choose the simple brush and then import. You could also use the multi append tool in subtool maser. Just select all your meshes and import, it does all the rest for you. Huge time saver!
Thanks for the replies and suggestions, guys.
Subtool Master. I didn’t even think of that, sounds like a much better option.