I used to run two independent signals through my
Rocktron hush unit about two decades ago. I ran an acoustic through one side and my electric on the other and they were certainly descreet signal paths. I think I still have that piece of gear in a closet somewhere. Rocktron makes some fantastic products. I don't know which unit you are using but I think your best bet is to check their site or even call them. I've called them before and they were very helpful.
Kent