I'm not totally sure you've diagnosed the situation correctly as an entry in the _output/templates/_metadata.json file shouldn't ever be referenced in that way. We only use the metadata file to compare hashes for the template watcher system and track the version ID and version string changes across version changes.
Essentially if an entry exists in the _metadata.json file, then it would be ignored. It isn't an inventory of what should be imported during add-on install or anything like that.
If you get an error on a page about a template not existing then it would usually mean that page is attempting to render that template. Is it possible you have a template modification trying to render that template, or a code event listener?