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From the small pool we have here it seems that it is just you encountering that problem, but yes the existing paths might be borked. You can try some of the extended commands like reorder, but I don't know if it will save you. Sometimes you have to start over (I have had to as well, but other reasons). After a while you should get the hang of just putting nodes down, processing and doing a second run to clean up bad pathing through testing and be done with it.

I don't see anyone fixing this issue with removing nodes anytime soon. Barely anyone touches the #path commands or code at the moment. There is only one server that has a complete set of pathing files which are 'proprietary' it seems.

As far as the commands you noted, I would stick to connect/disconnect/add. Those are the ones you need and then use process/dump as previously instructed.