@Zachary-Lowell-0 Got it working. It seems we encountered a documented bug where the defaults were somehow getting incorrectly set to the wrong parameter for RC input protocol when we reset the board to firmware defaults. We were checking the COM_RC_IN_MODE but had always had the RC_IN set to Auto previously. This made everything look fine until it glitched and changed the parameter without us knowing.
In case anyone else runs into it, here is the bug: https://github.com/PX4/PX4-Autopilot/issues/22986
Appreciate the assistance on figuring this out Zachary, we can switch over to Flight Cores and VOXL Flights for this client now which they'll be happy about.