One thing to check into in this regard;
SOMETIMES, the CNC machine needs the neutral of a 208V 3 phase 4 wire feed, because they are tapping off from phase to neutral for 120V control power going to the electronics or other controls inside. When it was DESIGNED for a 208V Wye system, they could have tapped off of ANY phase to neutral and it would be fine. But when it was hooked up to the 240V 4 wire system, you can only tap from A or C to neutral to get 120V, but there may be something inside tapped off of the B phase and that is what is getting damaged. If so, all you really need to do is either move that connection to one of the other phases, or just use a 240-120Vcontrol power transformer to power everything. I've found this issue more than once in similar situations.
Motors on the CNC machine are usually driven by servo amps or VFDs and do not care whether it is 208V or 240V, the sensitive part are really just the controls and the power supplies for them.