Same issue here, I use two peripherals (in my case controllers of Saitek Cyborg joysticks) that have the same name but different deviceIds in Windows.
MSFS 2020 kept these two apart, so stuff configured on one controller did not affect the other.
Now in 2024, randomly when starting MSFS the control bindings of one controller seem to move to the other one. Apparently MSFS 2024 does not include the deviceId when keeping track of devices but only their names, resulting in this mess.
As I said, MSFS 2020 had no issue here, neither do other tools like AxisAndOhs. It’s just a regression in 2024.