I don't think there's a way to do this in the GUI.
I had a quick look to see if it would be enough to change the "map_type" in the "network_maps" table in the database to "0" for the map in question (based on our table it appears that 0 = Custom, 1 = Layer 2, 2 = Layer 3) and to remove all seed nodes from it - the result was that the map I was testing with became extremely slow to work with (and ended up with over 3000 links, rather than the 30 it had before - most likely the reason for the speed issue). Changing flags to match another custom map did not help and I ended up wiping the map.
There may of course be a safe way to do this if steps are taken in the right order, but I am pretty sure it's not exactly "supported" and may trigger all kinds of unwanted side effects.
I had a quick look to see if it would be enough to change the "map_type" in the "network_maps" table in the database to "0" for the map in question (based on our table it appears that 0 = Custom, 1 = Layer 2, 2 = Layer 3) and to remove all seed nodes from it - the result was that the map I was testing with became extremely slow to work with (and ended up with over 3000 links, rather than the 30 it had before - most likely the reason for the speed issue). Changing flags to match another custom map did not help and I ended up wiping the map.
There may of course be a safe way to do this if steps are taken in the right order, but I am pretty sure it's not exactly "supported" and may trigger all kinds of unwanted side effects.