This is a really interesting problem; I feel like there's a range of solutions. First thought would be to take some sort of sensor checkpoint if you have full motor cutoff. Also wondering what the options are for soft-reboots that don't drop telemetry connections to your control hardware.
Yeah, I'm hoping we can get around it with just a telemetry command (we've got two-way telemetry radios) to reset the EKF state.
Full motor cutoff/checkpointing is a fun one. One thing I've found that seems to seems to exasperate the issue is picking it up when it's on the ground, adjusting a camera or something, and putting it back down on the ground. That's an almost guaranteed way to get a "high accelerometer bias" or "compass skew" error.
