Skill tree fails to hold changes after respec, and has permanently "lost" me a skill point

I have been trying to respec my skill points which will lead me to have a different path to the same nodes. I previously went south, and now I want to go North.

I respeced by unspeccing from some nodes I wanted to give me extra points. I then connected the new path to the node I want, and start disconnecting the old path. I made all the changes and it seemed ok.

For some reason, it looked fine but I couldn't socket my new Jewel into my new Jewel socket. After a minute of trying, the whole tree had reset to before I made the changes (but kept the gold cost).

I then tried again, and it still did not work. Upon deciding to give up and just leave my points, when putting them back into the nodes I unspecced from, I am now one point short of where I started. I've quadruple checked and I've almost certainly "lost" a skill point