You need to define an end state. This is the state all units end up in after the cinematic completes. It is very important you define this state to be highly deterministic as otherwise skipping a cinematic could give player advantages or cause strange bugs.
Thus for every cinematic, I advise you create an ending trigger. This trigger performs the end sequence of the cinematic and makes sure all units that the cinematic touches end up in their proper positions and states. This trigger is run either when a player skips the cinematic, or if the cinematic is left to run to completion.
Cancelling on-going cinematic triggers is either done using a check after the thread wakes up from a TriggerSleepAction or using the trigger queue system (I think that is how Blizzard did theirs?).