Prevent Mass Deletion
Mass deletion of synced libraries should not be as straight forward as it is today. At the moment, if a user with contributor permissions deleted a large number of files, they will only get an email afterwards informing them that the files are available in the recycle bin to be restored.
Say the document library had 30K files which are now in the recycle bin, restoring those would take a lot of time.
An alerting and approval system should be in place. For example, if a user started deleting files from a synced document library, at the 100th file, an alert should be sent to the SharePoint admin and to another point of contact to allow the user to continue with the deletion process, or stop the action immediately.