Hi,
If the master caution is on check below for warning lamps and see if "TRF Failed" is on. If so the only way to rectify this is a complete restart of FSX. It is due to simconnect loosing communication w/ FSX. Most problems with the inability to set the reference is due to a joystick / yoke not centered in the axis you need to engage the AP in, (Roll/Pitch) or the lack of a wide enough null zone where noise gets sent into the AP and it thinks you are requesting "control steering".
Roman