Welcome to the forums. I have no idea what that bolt is for, but I don't think you hurt anything by taking it out. All the transfer case has inside is just two big gears and the shafts and bearings they ride on. I'm not even sure those bolts go all the way through to the inside of the case.
Most 4-wheeler problems are caused by a loose nut connecting the handlebars and the seat!!
You only need two tools in life -- WD-40 and duct tape. If it doesn't move and should, use the WD-40. If it shouldn't move and does, use the duct tape.