I'm very new to CNC so I'm still learning A LOT. But you've touched on a problem that we've been trying to figure out. We are running a CNC router doing a lot of 3D designs and have had problems with a fuse blowing occasionally and ruining a part. Inevitably, on a design that does 3 roughing passes and then a finish pass, it's usually when it's at least halfway through the finish pass that something goes wrong, and like you said, one axis quits but the other two keep going and you're totally screwed.
I heard somewhere, (I can't remember where), that there was possibly some way to hook up the Geckos so that when one dies the other two stop, (without doing a E Stop). If you have a good solution to this problem I'd love to hear more about it. It is a horrible sinking feeling when you go in to check on the machine and you see one axis not moving.
Thanks in advance for any suggestions!