Perhaps have a ABAP developer review the code within the transport to verify what commands/updates are transporting to the prod system.
Also is this a Dev SolMan -> QA Solman -> Prod Solman transport path? Does this issue occur between Dev/QA?
It may be possible that you have an overtaker transport effect happening, and a different and possible unrelated transport is updated the object version of your Prod system and when you transport the template it reverts the object wiping out previous information (notifications) and referencing a previous object making it look like prior transport kept the notification settings (object).