During mash in and/or your protein rest (in any case before you pull the first decoction) the majority of the enzymes have gone into solution, i.e. they're in the thin part of the mash. When you pull the thick part of the mash for the first boil, you'll of course bring some amylase enzymes into the the boil kettle, which will be denatured when you boil, but not to worry, the workhorse amylase is still in the mash tun safely waiting to be brought up to working temperature.
When I have done decoctions, during the boils before saccharification (in my case, the first boil), I follow Kaiser's instructions and do a mini-saccharification rest in the decoction kettle, just to make sure that during saccharification of the main mash there is the appropriate amount of enzyme to starch.
Point being, the enzymes in solution in the mash tun don't get boiled, so they're still able to catalyze their reactions, and truth be told, they are probably sufficient, given time, to convert all of the starch in the mash without the mini-saccharification rest.
