Ok, we all know after reading chapters 54 & 55, Ed and Al can NOT do Alchemy right now. Well, what if by the Father "touching" them when he healed them, he in fact interrupted the "circuit" that allows for the alchemy to work without any sort of transmutation circle (a.k.a Clappy XD).
Now this may seem a little farfetched, but hear me out: If there was a case of there being a field that inhibited ALL alchemy, then Scar and Mei would not have been able to use alchemy either. But no, neither of them were affected, and the Father was completely baffled as to why.
If you take this into account, then you have a soild case stating that if the Father really DID flip whatever "switch" into the off position, the brothers are pretty much screwed in the alchemy department (But we won't know if this is the case until they get completely away from the Father).
It wouldn't be a great thing for this to happen, but these are only my theories about what may come to pass of things follow a logical progression in dealing with this subject.