Have there been any changes to the vx3 or yaesu cloning code in the past few weeks? I took a quick look at hg and didn't see anything which seemed applicable and it could just be random coincidence (as I've purposely written bad data to these radios before and never got a result like this), but if there have been any changes recently they likely need to be reverted asap.

Nope, no changes. I, like you, have written mounds of bad data to them without any trouble before, so I expect it's actually something else. Have you checked that the charger is actually working and checked the battery voltage in the radio? Those little switch-mode power supplies fail now and again with the usual capacitor type issues.

You might also try a full reset procedure, although it sounds like maybe it seems a little more dead than that.