Versioned settings in branches after TeamCity update

I'm considering storing TeamCity project settings in Git to simplify the TeamCity structure and allow for easier reuse of the builds for multiple source code branches. According to the confluence documentation, this should be possible by using the option "use project settings from VCS:". But I am not sure how this works after a TeamCity upgrade. 

I understand, that the synchronization with VCS is disabled after upgrade and must be enabled manually (btw some option to override this behavior could be helpful). But what happens after I re-enable the synchronization with VCS? I suppose that TeamCity will commit the configuration in new format to the default branch of the VCS root. But what happens with the configuration in other branches, such as the master branch with production code where the TC project settings could be different from the the main develop branch? Will the TC update also the format of the settings in these branches? Or will it be able to work with the old format?

I just hope that the TC upgrade does not mean that the project settings in branches are suddenly useless and that I must somehow manually migrate them to make them work again. In my opinion, this is worth clarifying in the TC documentation.