This seems like a bug, but I may be missing something. Here are the steps I follow:
1. Change to a new version in my published utility network service.
2. Find I want to attempt a change that requires network topology to be disabled.
3. Execute the "Disable Network Topology" GP tool. This completes successfully.
4. Want to re-enable so I attempt to "Enable Network Topology"
5. This results in an error with the message "Operation is only supported on the DEFAULT version"
6. When I return to the DEFAULT version I see that Network Topology remains enabled, just like I left it.
So it seems its possible to *disable* network topology on a version below DEFAULT but not possible to re-enable it. If I've missed something any pointers would be much appreciated.