Not all the lines are high pressure but would not know which is which without seeing how things are plumbed. My guess is they removed the filter for room to put the remote valve although the filter housing is not built into the transmission and could be located anywhere.
Did they give you the housing and filter back? If not, I would definitely ask for it. You paid for it when you bought the tractor and I doubt they gave you credit for it when they added the remotes.
Getting advice from another dealer is a good idea that oldnslo suggested.