Any later than 3 weeks into flowering and cutting anything that significant off of the plant is ill advised.

1.) It stresses the plant stunting growth and potentially causing hermie
2.) The clones will be very late into flowering and will present issues going through the reveg state
3.) once rootings are cut dip and have a layer of exposed cambium then they can be dipped in a rooting hormone (Gel or Powder) and then stuck directly into a 50/50 mix of vermiculite and perlite under 24 hours of a very soft and gentle light (one low wattage flourescent)

Hope this helps,
SMG