Well the fact that the conductors were disconnected and re-connected gives good reason to investigate that there could have been a phase reversal. However I have seen intermittent phase sequence mismatch shutdowns on 2 brands of generators. Same power system. No changes. Just at random. Sometimes it's a controller firmware issue that causes intermittent tripping. I also have a hunch that if there's changes in load or voltage right at the time it is trying to sync that this could cause some controllers to trip. If you're confident there were no mistakes in anding the cables then contacting the manufacturer may be helpful.
Is this a medium voltage generator? If so you might be doing phase sequence checks on the secondary of a potential transformer. Did you have someone verify phase sequence before the cables were removed?
My opinion is that it is better to use "phase sequence" or A-B-C instead of "phase rotation" because some engineers I have interacted with think automatically of "phasor rotation" in which phasors are graphed out at counterclockwise rotations. This company makes a meter that spins CW on ABC and another that spins CCW on ABC. You buy the one that makes you feel best!
.