On the documentation page for $out (https://docs.mongodb.com/manual/reference/operator/aggregation/out/) there is no warning that running the stage on a collection with an existing Atlas Search index will delete it. Under the "Replace Existing Collection" section there is a potentially misleading statement: "The $out operation does not change any indexes that existed on the previous collection."
There are a few sections on the $out page that could warn users against using $out and using $merge instead where Atlas Search indexes are involved. These are "Comparison to $merge", "Replace Existing Collection", "Index Constraints", and "Restrictions".
Compare https://docs.atlas.mongodb.com/atlas-search/index-definitions/ where the impact of $out is highlighted near the top of the page.