Olaf Fritsche:
The question would then have to be which of two interference effects is greater:
1. if the corrections due to autoguiding are greater, it would make sense to turn it off during focusing.
2. if the tracking errors are larger, autoguiding would support correct focusing.
Does anyone know which confounding effect predominates with good PA?
Or am I making some kind of thinking error?
Typically autofocus exposures are on the order of a couple of seconds (for my fast F2.2 system) and probably not much longer for most since I get quite a lot of stars using a guide scope. This may be different with an off axis guider. So unless your polar alignment is really bad, your drives are really balky with much periodic error, or something of the like, then I think turning it off is thought to be the safest bet. The way I set up my guider is to use 1.5 or 2 second exposures from my guide camera and then the software makes an adjustment via a pulse to the mount. So think of it this way; if that pulse happens to occur during one of the main imaging cameras 2 second exposure, then the stars may all be streaked, even much more than from some slight tracking error.
Also, consider that if misalignment is not good and the errors are consistent, then short streaks would result. But if you think about it, this is not fatal because the HFR or other determination should still find the "best" number, which is all relative anyway. So still in focus.