Yeah, meanwhile I found the culprit. I calibrated my HOTAS in Windows as Mandrak suggested while talking about all of this. It stopped working again. I erased my joystick.cal file in Config folder so BMS recreate it, I checked my axis in BMS setup, and it works again. Here’s my culprit at least.
OP, if you want to erase your joystick.cal file and check.