If you've never topped photos before, don't top autos.. To get a good result, you'll either need experience or extremely good luck.
To answer your question tho.. If you absolutely have to top an auto, don't do it later than the middle of week 3, since most autos generally start flowering around week 4.
- It will recover, but if you do a bad job at topping, it could take a week or more to do so..