Transplanting hydro to soil. Can I break roots to remove perlite?

Get a 5-gallon bucket and half-fill with warm water. After removing plant from hydro set-up gently swirl the plants' roots in the water until rootball is up to your standards.

Good luck, BigSteve.

Do what you have to. If you remove a third of the root remove a third of the vegetation. We all have screwed up at one point or another.