This is because configs/NpcSpawn_old.json still exists from the last time you updated NpcSpawn. If you are done with that file then you can delete it, rerunning the upgrade will complete.
@CsaszyKJ That will work provided the config file layout didn't change - but if it did change it will leave you with a broken NpcSpawn configuration. It's likely to be fine most times, but I wouldn't recommend unless you know the config layout didn't change. In any case, it's better to resolve the root problem since it is easy to do as mentioned above.
@KpucTaJl I understand why the old config file is not auto-deleted and agree with that decision. With that said, could it be a good idea to detect this and notify the user that the upgrade was aborted due to the old config file still existing from a previous upgrade?