I think it was just malformed XML last time I had it happen. That certainly should be preventable (or at least less likely to happen) using an app than manually editing.
very interested to see how you come out with this. I've setup my app launcher with folders just the way I like several different ways, but any time i mod hildon.menu, cpu usage ramps up to about 4% at idle. No big deal, but it pulls on the battery overnight. guess i can make some "Good-Night" and "Good-Morning" scripts but it shouldn't be that way. are you far enough along to see if this bumps up hildon-desktop activity at idle?