One of my colleagues replied with a suggestion in the group email. I agreed with his suggestion. The other colleague in the group responded "perfect - lets fold that in Andy."
"Folding in" means incorporating the change. It is used when the speaker wants the idea integrated into the existing product, rather than simply being tacked on.
There are many potential etymologies, but the one which makes the most sense t me is one from cooking. When making a dessert such as a mousse, you often rely on beaten egg whites to provide the airy texture required. However, you cannot simply beat the mousse after adding -- it would not result in the appropriate texture. Instead, you beat the eggs separately, and then incorporate them with "folding." This folding is a complicated maneuver with the spatula, which is best explained by watching a youtube. However, the effect is the part which is applicable to you: it ensures the foamed egg whites are evenly dispersed throughout the mousse, but doing so gently enough to not crush any of the foam bubbles.
Compare this to "Perfect - let's cram that in, Andy," which would imply that you would distort the suggestion until it fit into the existing pattern (possibly disrupting the original purpose of the suggestion). Also compare to "Perfect - let's put that on top, Andy" which would suggest putting the suggestion in play, but not trying to incorporate them. If you put it on top, there would be the possibility of tearing it off later if it didn't work. If you fold the suggestion in, it should be harder to separate.