When removing a node from a cluster, the procedure is to comment out the node entry in the nodes file on all the remaining nodes in the cluster. There does not seem to be a procedure to actually remove the entry from the node except for shutting down ctdb on all the nodes that have a higher number than the one shut down and rename the tdb files manually before restarting ctdb.
This is working as designed. The node numbers (PNNs) are core to CTDB's operation and can't be changed at run-time.
Commenting out a node in the nodes file marks the node in that slot as deleted and works just fine in combination with "ctdb reloadnodes".
In the future we could consider a richer syntax for the nodes file where the PNNs are specified along with their address, but this isn't a high priority.