As noted, if the robot is partly in Base, then there's no Robot Penalty for touching it (Rule 43), but the robot will need to be restarted to continue.
The robot is allowed to be in contact with a mission model when you rescue it--however, Rule 49, Chain Reactions, and Rule 50, Reversible Changes warn against making changes to objects outside Base when the robot is offline.
Rule 8, Mission, says that the team gets to decide when to do what, and may retry missions, but the field is not reset if the autonomous robot has changed it.
VA-DC FLL Referee Advisor
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