Not sure if this is recommended or not, but you can have templates part of your code package, so even if it gets wiped out, it will still get installed on next code deployment.
Also you can follow a complete custom hierarchy for e.g: /etc/<your-app>/workflow/notification/email/<use-case>/en.txt
Adobe pretty much uses same technique to differentiate different workflow email templates -
/etc/dam/workflow/notification/email/downloadasset/en.txt
/etc/notification/forumdigest/default/en.txt
/etc/notification/messaging/default/en.txt