Haha, I just went and looked because I hate not knowing. Scar does it in the beginning of chapter 106 - talks about negating the "cushion" that is made up of the souls and freeing the energy of the earth's crust.

So there were two counter arrays - one by Hohenheim to counter the making of the Amestris Philosopher's stone, and one by Scar/Scar's bro to free up the energy. Considering the alchemists fighting Father had no issues with the transition, I don't think any other alchemist would have problems either.