The issue really isn't that it's not backing up the folder (which I can see an argument for both sides and various ways to do it) - it's that they changed what

The issue really isn't that it's not backing up the folder (which I can see an argument for both sides and various ways to do it) - it's that they changed what they did in a surprising way. Your backup solution is not something you ever want to be the source of surprises!