Generally speaking target_activate and _deactivate control whether something can be triggered (activated) or not, like their names suggest. So, logic alone dictates they should have no bearing on whether something that's already moving stops or continues to move. Rather, they control whether you can trigger it anymore to change the behavior or not.
If you can come up with nothing else, you can have a look at the rotating doors tutorial that some bloody n00b wrote a long time ago. It should be easy enough to apply to make what you are trying to make.
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