I tried to reproduce your problem.
Yes the wires are not deleted if you change the connection within the schematic. (That’s annoying.)
I don’t have a nice workaround for that. The only thing you can do is delete the wires that are effected. I’m not sure if this problem can be easily fixed.
In my tests, DRC always tells me that something is wrong. (Errors: “Two track end too close” and “Track near pad”)