I've recently started a hyro setup for the first time and did just that. The two well established clones took but I could see where you might have to factor in failure from virus, fungi, and molds.
I let the plants dry out and gently broke off all the soil and carefully worked the rootball up to the rapid rooter. Once I was happy it was clean, I washed out the roots in plain ph'ed water and planted. Worked fine but I've got second system to keep them in hydro start to finish now.