Personally i think, that if you are getting toward the end of the grow cycle, since you are flushing i would assume is almost ready for the chopping block, Then no i don't think it would hurt it at all. I would just pull it out during the start of the light on cycle and start the flush let it sit in the bath tub for a few hours to make sure its drained out pretty good, then just pop it back into the tent. If you are flushing then you more then likely only have 2 to 2 1/2 weeks max untill its finished
Cannabis in general is pretty resilient there isn't alot of things that it can't bounce back from especially in soil