WalterT Can you share how you check the FWHM in the AAP, and also what about that number tells you if you need to refocus or not.
When I first start tracking on my target for the night, after focusing, I'll take a 3 second image in Preview mode.
When this image loads, I select Tools->Detect Star.
This will take a sample of stars in the image and calculate and display the average FWHM value.
This can vary with the seeing on the night but for me is usually around 2 arcsec.
If your focus drifts while collecting subs the FWHM value will gradually change.
I'll check FWHM occasionally as the subs roll in. The first sub will be a little higher than 2 arcsec, just because the sub is over a longer time and the mount accuracy is going to play a part, but they are generally around 2.1, 2.2.
If the subs get to around 2.4 I would probably be rejecting them when processing so I would refocus at this point.
As I said, I rarely have to refocus the SCT within the hour after auto focus, and AAP is set to finish focusing with a CCW movement and autofocus every hour while ion Autorun mode.