You absolutely can, but it will hurt potency and yield. I have kept mine on an 18/6 schedule throughout.
If you have stealth reasons or energy concerns, they will do fine under 12/12. Otherwise stick with 18 hours or more of light.
no part of the benefit of autos is the ability to run 16-20-24 hours of light during flower. 18 seems to be the most common number for auto flower growers...