I have a slightly different problem. Though it's probably solved by the same solution pintocat posted. While using GEM, a Scout can get an event or ruin or whatever that gives a choice to either clone the Scout, or turn him into an Archer with ITC promotion. That's fine and dandy, in my book. The problem comes when upgrading the Archer. The promotion gets lost. Sort of makes that earlier choice useless. Would rather have chosen to double the scouts if I knew the promotion would disappear. Of course, there's no indication that it will disappear when you first make the choice.
Anyway, burned once by that, now I'm using pintocat's solution.