Sure! Just select all the FileOut nodes you want rendered and then, from the menu, choose Render->Render FileOut Nodes…and select either “selected” or “all” (which obviously overrides your selection) in the Render dialog, depending on the need.
One caveat though, is that all the FileOuts will render out the number of frames you have specified in the Globals tab. For instance, you cannot have FileOut1
render 50 frames and FileOut2 render 100 frames from the same script.
I think there are ways of doing this through the command line but you’ll have to search the forum.
Otherwise you shouldn’t have any problem.
Good luck!