The salt-minion backup delivery mechanism (the agent that runs on your server) deprecation was first announced on August 1st, 2016 in favor of the SSH method. The SSH method is much more stable, fast and reliable.
To upgrade a server simply edit the server record and add the necessary fields (ip or domain, port, user, operations directory) etc. Once you save the server an SSH key will be generated. You can add it to your authorized_keys file for that user and refresh the connection status on the view server screen to verify SSH can connect.
If you are missing any dependencies for the backup operation Ottomatik will attempt to install them for you, however if it is unable to do this you will get a backup failure notice with details.
The link above can help resolve questions along these lines, and you can manually install the dependencies according to the directions found at the following help article.
From there you should be good to try an on-demand backup and if that works then your backup schedule should continue as usual. If your account doesn't support on-demand backups a quick trick is to clone and rename an existing backup as a test providing 24 hours of on-demand for that job.
Once you have SSH based backups running you can uninstall the salt-minion.