Despite making sure I have not set software limits on the AZBox, I've found that the usual failure mode is for me after scanning appears when I try to move east. After just a few degrees, I will hit the AZBox-set limit and the dish stops moving because it has hit the software limit. I originally thought that every position had been corrupted and I would do a complete reset. But, a while ago, I tried just clearing the limits. That worked without deleting any of my positions. These days (at least for me), it's more of an annoyance than anything else. If I'm really on the ball, I will move to the spacecraft I want to scan or the new spacecraft I want to add and simply manually turn off the GBox while I do the scanning. If I remember to do this, the AZBox doesn't set software limits for some reason.
Finally, it's a good idea to write down your known positions. If you have to do a re-set, you will at least be able to come close reconstructing everything. I made up an MS Word table that I find useful to document my settings. When I get home tonight, I will upload it in the hope that others might find it useful.
Oh yeah -- don't forget to frequently BACK-UP, BACK-UP, BACK-UP!