I just ran into this issue again (one 5.2.0), one of my VMs is not deploying because of this. As you mentioned, the config that was generated probably several versions ago contains a port number, so I guess that’s the problem. Recovery is easy, the only problem is that it is not intuitive for an unexperienced user 
From the administrator’s perspective, I don’t get the following: The port number is exactly the same as would have been calculated by ONE (5900 + VM_ID). Why is ONE thinking this port was already in use? I searched the database, there is no other VM with that VNC port.
I think, the open questions are:
- Is this a bug? My intuition says yes…
- Would it work to remove all VNC ports from entries of undeployed VMs from the database?
Greetings