I can't offer a fix, but wanted to add that I have the same issues and have posted a few threads and feature requests.. I think it's becoming clear something is not working right a portion of the time.
For me, part of the issue is I image with filters... and my last failure was because the autorun was on 6nm OIII filter, and you can't find any stars at 2800mm focal length with that narrow of a filter... so it's filtered and maybe sees 10% of the stars, not enough to plate solve as it looks just like a cloud covered sky to the camera.
The second issue is what you are experience (I have an EQ6R Pro and a CGX) both have failed to resume imaging after a meridian flip. and I've found that home is WRONG after the flip.... the flip isn't just shifting sides, something is becoming out of sync. after a flip my goto's can point in the dirt instead of the sky. One user in another thread has been saying that maybe the pierside data is part of the issue... so check the other threads here posted during the week and follow some of those, even though they are for other mounts, I think we're finding the issue isn't the mount.