Where is the other one?
one is in
pi@Raspberry:/home/pi/.node-red/
and the other in
pi@Raspberry:/usr/lib/node_modules/node-red/
That one is the default that is provided when you install node-red. When you first run node-red that is copied into your working folder (/home/pi/.node-red in your case) for you to adjust as necessary.
thank you for clarification
Hey People having this type of behavior. I had a problem that sounds just like this and I found the problem to be I needed to logout to release the token.
It would just login.
Here is a thread to help those who need to solve this issue.