If they are vegging, I would just let them be, I think a little abuse is good for the plants. My last grow went threw a tropical storm, and I just let it take the hit. get those stalks nice and thick : )

But overwatering is a bit of a problem, if you have good drainage ( perlite, etc. ) you should be alright, but If you already have the greenhosue made, I would just leave it in there

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