to reproduce the error you can do:
- Create a new Pipeline job
- In the job configuration, choose "Pipeline Script from SCM"
- Enter a existing git repository URL (and credentials if required) containing a Jenkinsfile
- Select "trigger from SCM and enter a time"
- Wait until job gets triggered (I let the job fail on purpose by providing a incorrect Jenkinsfile, but for this issue I think this is irrelevant)
- After job got triggered go back to configuration page and change the repository URL (containing a different Jenkinsfile)
- Change the trigger and wait until job get triggered
- Now have a look at the query protocol. My protocol indicates that jenkins is still using the first repository:
The same seems to account for the other values entered through the web interface (Name and RefSpec).