Hi Scott,
Not something I have personally tested, however the process I describe above is intended to minimize downtime. If you do the Primary first, you would need to either shut the backup down, or it would become Primary when IC stops on the Primary, so you would still have the same problem.
I would propose that a better solution would be to make sure the custom folder is added to be synced up, if it isn't already. That way, you don't care which is Primary (although you would need to make sure you save updated handlers to the currently active one when developing / deploying.)
Also, and I'm not certain about this, but I believe that the upgrade process doesn't deploy a Handler that has been modified on the target system. That means that modified customization points shouldn't get "reset" by the upgrade. I need to check that out, though, and that's a bigger job than it seems!