The recommendation is simply that your delete your local clone of the org.eclipse.tycho.extras Git repos.
Your contributions for tycho-extras plugins are still welcome, using the usual Gerrit workflow, just the repository URL changed. Since repository keeps history, you usually can cherry-pick or push your pending commit from former tycho-extras Git repo to the main tycho Git repo, and that should work without trouble.
The branches and tags for tycho-extras are currently still part of the (now read-only) legacy tycho-extras Git repo. As long as there is no value in copying them into the main repository, they're likely to stay there.