Autos will continue to grow through the flower stage. By pruning the way you did it’ll slow down the growth until the plant recovers. Which is OK with the photo plant but auto‘s internal clock keeps ticking
Because of their fast lifecycle it is also recommended that you don’t top and prune Autos all that much. The general rule is more of leaf leaf tucking. If you out of time with the flower cycle I would extend you have lots of time to go still.
Majority of my experience is with photo not autos.