The problem is not really related to AOFO.
BE 11d has split the System State and Shadow Copy Components in two. So all of the jobs are looking for the Remote Agent to understand the separate components of the backup job, which BE 10d agents don't.
So you don't actually need to do anything other than realize that until the remote agents are updated the System State and Shadow Copy Component backups will not function.
Otherwise, yes you will need to upgrade all of the remote agents to rid yourself of the error and failure.