After a crash I got the above message. I tryed to reset ardupilot with the newer firmware version, but the erro remains. For some reason I have no idea why, I uploaded my pixhawk 2.4.8 with px4_fmuv3 and apparently it did work (i did not try to run motors, but qgroundcontrol prompted no errors).
Tryed to return to ardupilot firmware, but the error message still there …
It is possible that there is a mismatch in update logic between IO board versions. You can force the update by holding the safety switch button during the boot.