Edit: I think I found the issue. In the 2025 documentation (https://docs.safe.com/fme/html/FME-Flow/WebUI/Version-Control.htm) this note has been added “FME Flow currently supports only GitHub as a Git repository.”. Since my repository is on Azure it no longer works. 

I will leave this here, because I'm probably not the only one that will run into this issue.

----original post:

After update from 2024.2.1 to 2025.1.2 Version control is not working anymore.

The issue is sort of the same I had last time: 

Only this time when I press Push to Remote I get the message “The remote ref update was rejected. Check your repository permissions or configuration and try again.”.
I refreshed the token to be sure the right token is entered, but that did not help.

I opened the repository with Visual Studio Code on the server (D:\ProgramData\Safe Software\FME Flow\repositories.

The check-out branch is main and it says there are 125 changes. The branch is not published.

Because last time I figured out the FME Flow only uses the master branch, I wanted to checkout the master branch. But to be able to do that I had to commit or delete all the changes. I deleted them and checked out master. Apparently this branch is not published. So I tried to publish it, but i can only publish it to Github.com. My repository is on Azure DevOps. I have no idea how to change Github.com to Azure DevOps.

I use an express install and after the upgrade I restored my backup. Clearly the backup is not equipped to restore this, like it is supposed to.