I'm tagging this as a child issue of #2386530, as the patch for that resolves this, but the problem may be deeper, and should maybe be considered in pathauto itself? It may be unlikely that future updates are made to this module, but wanted to make sure this was there for someone running into the same problem as me...

When pathauto_entity reacts to a comment being deleted, it calls "pathauto_entity_path_delete_all" for the comment. From this, pathauto looks up the URI to the comment via entity_uri, which happens to be the URI for the node as well (just with additional fragments to get to the comment). Then it runs delete all on the "path", which removes the node alias. Applying the patch from the tagged module resolves this (unless you are using pathauto_entity for comment entities).

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matthensley created an issue.