Currently, the GitHub integration can't be set up with multiple instances, which means that only one instance is owning all entities.

This becomes problematic when you want to have two kinds populate the same entities. The reason for that, is the query field can result in an entity being deleted from the "enriching kind" rather than the "owning kind".

Suggestion: Add to entities created by the GitHub app a new type of ownership, based on the mapping kind. This will allow only specific kinds to delete entities from the catalog, while allowing other kinds to safely "enrich" the entities.