I normally grow Photoperiod strains, but I have friends who grow Autos indoors and outdoors. I don't think you necessarily damaged the roots, but from what ive been told Autoflowers/Ruderalis Strains just don't like to be transplanted at all and that transplanting can actually stunt growth whether you damage the roots or not. Best to start them off in the pot that they'll finish in and because they don't generally grow too big you'll only need an 11litre to 15litre size pot max. Hope this helps mate