Protocol selection now has a confirmation step. When you click a protocol card, the other two dim out and you get a CONFIRM / CANCEL prompt at the bottom. The confirmation text makes it clear that your protocol choice is permanent for that save slot, not just for the current prestige run. If you want to try a different protocol, you need to start a new game in another save slot.
The warning text in the selection screen has been updated from "irreversible for this run" to "irreversible for this save slot" since "run" was causing confusion.
Once you've selected a protocol, you'll also see a small LOCKED badge next to your rank in the protocol rank strip, so it's always visible that the choice is set.
Thanks to MAKAIROSI for flagging this one. It may change eventually.