I’ve had trouble with the meridian flip goto failing my last few nights out. I’d wake up in the morning to the mount being in the position it would be in pre-flip, and, only this last time, did I go out and observe it acting up. The declination axis would only turn a little bit and the right ascension would turn about half the way, start a horrible whining noise, and then stop. The mount would then go back to where it was without fuss.
This happened during the automatic meridian flip process within APT. When I perform meridian flip gotos manually using Stellarium commanding EQMOD, everything would always work correctly. I’m not sure if the goto issued by APT is different or is performed differently than other gotos, but it’s failed on my three times in a row now.
It seems there are some settings that need fiddled with in EQMOD. After changing the settings, I did a clean test with a random object at high altitude right before it crossed the meridian. APT successfully flipped and retargeted it. The meridian flip on my next target that night worked out perfectly.

In the driver setup page, change the ASCOM Options ⇒ SideOfPier to Physical.

On this screen, make sure Mount Limits ⇒ Enable Limits is unchecked. Then click the wrench button in that section.

In the subsequent popup, you will want the Options all unchecked.