You probably deleted there more than you had to, but yeah, that's what you needed to do.
the part that says "MakefullyKnown(...)" are the ones responsible for your problem, so you'd probably just have to delete those parts. this is what it should end up looking as:
//for cloaking ships, we will have to change code below
PlayerFleetL1:=GetFreeSel();
SelectShips(PlayerFleetL1, s.race=#race_player);
m.PShipsCount:= AllNumOf(PlayerFleetL1);
This, however, won't be very kind to the AI, as it's not meant to handle cloacked ships, for example, it could happen that enemy ships will just sit there and won't pursuit, even after you revealed yourself.
And yes, changes on that file will affect the rest of the missions.