In the CCD module, will checking "Guiding Deviation <" abort the entire sequence or just the current image capture?
The help text says "Abort sequence if...", but that seems a bit of waste, doesn't it?
In my experience any of those boxes being checked affects only the current capture, or between captures in the case of focus. It could be that the sequence is aborted to stop further captures and then resumed? The end result though is my sequence continues after resolution of the limit.
In my experience you shouldn't tick that box at all. If guiding is bad then the guiding module will notice itself and will restart guiding. You may have a few bad frames because of that but imaging will not stop.