I don't understand how all this business of foam proteins getting used up applies to homebrewing.
If I shake the bejeezus out of a cold commercial beer, known to have good foam, the amount of foaming is limited by the amount of head space and the amount of pressure released(none). So I can shake it up really good and it can barely foam inside the bottle and therefore uses up little of it's foam-producing proteins. If I let that bottle rest a few minutes in the fridge, I can open it and pour a beer with a nice, lasting head. This is not theoretical because I just did it with a Stone IPA, which traveled 3000 miles on bumpy trains and trucks to get to me, being shaken(and probably warm) the whole trip.
Maybe if I shake up that bottle and immediately open it and pour out a gallon of foam, then let it settle and repackage and recarbonate, then maybe it won't have any foam proteins left. But in what scenario would that apply to what anyone would do to their homebrew?