Sorry, that's a bit outside my wheelhouse.
OK, I freaked myself out a little. This is what I want you to do (what I would do).
Take a video of each valve in action, moving all the way each way. Then after you swap, AND BEFORE YOU TURN ON THE PUMP, operate the valves, while referring to the video, and confirm everything is as it was: actuator bodies are oriented as before, handles are oriented as before, and the handles move as they did before.
The concern is somehow messing up how the valve gates move and ending up dead-heading the water flow. I don't think that's even possible, that's determined by how the valves are set up, not the actuators, but I'm just advising caution. If you're careful, you won't be messing with the valve gates, but if things get confusing and you (or the valves) somehow get turned around, there is a potential to get the valve gates in the wrong position.
Just go slow, take pics and videos and be sure when the swap is complete that everything is working as it should, as it was, BEFORE you power up the pump.
And as I said, this is sort of a desperate troubleshooting step. It'll be some work, and will determine where the problem is, but it's pretty involved and you might save it until you've exhausted all the other troubleshooting steps that you were discussing with Jim.