Couple things come to mind.

Did it really 'just stop' working?
How confident are you that nobody has either played with settings, or fiddled with the machine?

Without any photos, we can only guess on the setup. Could it be the encoder disc has spun on the spindle? It shouldn't but you never know. Is the encoder on the actual spindle, or is it belt driven of to the side?

Has somebody altered the spindle orientation settings?
A quick search of the manual reveals there should be a custom M19 macro to orientate the spindle, which is called automatically after the M17 macro, which itself is called prior to an M6 command.