I am not sure how “old” your checkout of sync-endpoint-default-setup is. If it has the certbot stuff in it, you should be able to rerun the init-odkx-sync-endpoint.py python script.
First stop your docker stack then run the script which should relaunch it. Also, it will try to rebuild containers to the latest so depending on how old might cause issues.
Safer option, follow this post on how to launch certbot manually (again if you are using the sync-endpoint version that switched to certbot).