I have noticed this behaviour, as I generated all branches to be able to checkout also 1.2-prime and 1.3-release and my testing release. All branches get created as expected. Afterwards when you clean-up or use a clean /var/trees/* dirs and run merge-all-kits for only single release - all your other branches get deleted from the repository this is expected behaviour as we are using git push --mirror

--mirror

    Instead of naming each ref to push, specifies that all refs under refs/ (which includes but is not limited to refs/heads/, refs/remotes/, and refs/tags/) be mirrored to the remote repository. Newly created local refs will be pushed to the remote end, locally updated refs will be force updated on the remote end, and deleted refs will be removed from the remote end. This is the default if the configuration option remote.<remote>.mirror is set.

reference: https://git-scm.com/docs/git-push#git-push---mirror

It would be nice to leave the other branches untouched and delete them only if for example --delete added to the command line. Don't know if it makes sense or not.
Don't mind if it gets declined as it is expected to run this way, but if using any CI/CD platform this has to be taken into consideration if only one release will be generated by the CI.