Yes, I’ve dealt with this exact scenario. Adding a countersink after forming is doable, but you’ll want to proceed carefully to avoid deforming the part, especially since you’re working with stainless, which is tougher than aluminum or mild steel. The safest manual method is using a hand deburring/countersink tool with a depth stop. It gives you full control, and since you’re only working with a 2 mm thick sheet, it won’t take much effort. Just make sure to clamp the part securely on a flat surface to prevent flexing while you work. Go slowly and check the fit with a sample M6 countersunk screw as you go.

If you have access to a drill press with variable speed and a good quality countersink bit, that’s another reliable option. Keep the RPMs low and use a sharp bit to reduce work hardening or generate heat that warps the part. Support the sheet fully underneath. Don’t let it hang or flex.