We experienced this same issue as well. We have hundreds of Endpoints and I was unable to find a reason while this was happening on a handful, but not all across the board. In addition to this, we had approximately 20 servers that were affected in which they started performing full image backups to cloud daily instead of incremental image backups.
Don't mean to dig at you guys, but this isn't the 1st, or even 2nd time something like this has happened to us. It's making me extremely hesitant to push out agent updates unless absolutely necessary going forward. We end up having to scramble to find a workaround. In this case the only solution was to manually downgrade each affected machine to the previous agent version. Can you PLEASE bring up the possibility of having the ability to choose the deployed version of the backup agent to the dev team??? At the very least, being able to rollback to the previous version would be invaluable for situations like this.
As it is currently, once you update there's no going back without disabling auto-updates. Then you still have to manually login into each endpoint and install the previous version. It's extremely time consuming, and not to mention as far as I'm aware, there's no repository to download previous agent versions unless you happen to have the installer stored somewhere locally, which thankfully in this case, I did.