I posted the following on the Tower (DroidPlanner) Git issue forum, and received a reply that this may be an ArduRover issue, rather than an OCU software issue. Interestingly, when I use MissionPlanner I don't seem to have the same problems - but I haven't thoroughly tested for it. MissionPlanner has the handy mission reset feature, which I use, and may be the reason why I'm not seeing it there.
Driving around last night, I aborted a mission by hitting hold and then RTL. I edited a new mission, and uploaded the waypoints. When I switched to Auto for the 'new' mission, the AP tried to go back to the 'old' mission's last achieved waypoint.
I cleared the mission in Tower, and uploaded no waypoints to try to clear it out. Then, created yet another new mission and uploaded it. Switch to Auto, and it still headed to the original 'old' mission's last achieved waypoint.
I let the asset drive it out to the end. Created and uploaded yet another 'new' mission, went to Auto, same thing. Only a reset of the PixHawk would clear it out and let me conduct a new mission.
Is this a Tower or ArduRover firmware bug? I'm glad I'm figuring this out with a rover, in a large parking lot with no obstacles...