I've experienced a similar situation last night. After the mount (HEQ5) finished the meridian flip, I tried to recenter the target objetc, but I was not performing gotos on the align module. Well, in fact it was performing gotos but only 3 or 5 arcsec at time (I've a big cone error and after the flip, my target was off but about 1/2deg). I interrupted the schedule, manually go to a distant object on the same side of the meridian and restarted the scheduler. It continued until the end of the night.