From what I could tell, you CAN save ability placements when switching disciplines. However, this must be done by making a loadout for discipline #1, e.g. Concealment Operative, and another loadout for discipline #2, e.g. Medicine Operative. Switching between loadouts properly saves the positions of abilities, but switching between disciplines within a single loadout does not save the positions. This makes sense, but a brief tutorial/explanation will save players a lot of frustration when encountering loadout/discipline swaps for the first time in this update.
To further prevent players from losing the position of their abilities, perhaps the game could ask players to confirm changing disciplines when the player already has multiple loadouts. If I want my character to change from Concealment to Medicine, and I have one loadout for each, then this confirmation window would stop me from switching my Concealment loadout into a second Medicine loadout.