Half dead

I got a plant i grew from a clone an i didnt have any net pots so i made my own out of a regular pot made for soil planting an didnt drill enough holes, so my plant grew to a V shape an now one side of it has stem rot due to moisture. Im 2 weeks into flowering can i leave the dead side an still continue with tha flowering as normal? I know my harvest for that plant will be cut in half litteraly lol. I was also wondering if i can still take clones this late into flowering?
 
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