Unfortunately if the files are gone there is not much we can do from the AutoMate side without a backup.
If this is a VM perhaps your IT team takes snapshots of the VM which you can revert to.
It might be worth reviewing the task file location that is set up within options/system settings/task service - default managed task location. Whatever path is set there is where the task files are being saved.
We are sorry we could not provide more assistance.