Yes, but the instructions for when you have only one remote include waiting for something like an hour between some of the steps. This is to prevent someone like a valet from cloning your key. If you don't wait for the required time then I can easily imagine the car would go into theft lockdown on the assumption that whoever is trying to set up the new remote is not authorized.The difference is that you had two working remotes. The instructions are different when you only have 1 and trying to add the second one. I think others have said when you have two working remotes and adding to it works fine
Note that in on Canadian Bolts you can't program a new fob unless you have two authorized fobs.