In response to the original question - the robot controller, while disabled, continues to run as if it were not. The only difference is that there is a flag set in the data provided by the operator interface and the master processor holds all outputs to off. Same with autonomous - the user processor continues in exactly the same manner, except that there is a different flag set and the master processor holds all inputs to be off. As far as I know, there are no processor resets initiated at any time during the match.
What this means for your autonomous mode is that if it becomes disabled and then later reenabled, your robot is likely to proceed exactly as if it had never been turned off at all (except that it will be in a different position)
This is obviously not always true, but it's probably a good starting point. However, as everyone else has been pointing out, there's no substitute for testing!
