The only thing I saw that didn't like the Concern I used were the pistils. Some suggested that I not spray those but thrips are notorious for running and hiding in secluded areas (like flowers) so I sprayed them down. Burnt the tips of the pistils but you can't see any now after a few weeks.

I would almost suggest taking care of the mites first and then cutting. Then there shouldn't be any problems with your clones, but I've never done clones! Well I have one I call Frankenbud that I'm experimenting with. Hacked it off 21 days into flower and stuck it in a glass of water. I saw where a guy laid out exactly how to do this for cloning so thought I'd do some R&D with a flowered shoot to see how it works.