You can inspect your local remoteStorage (IndexedDB) database to get a better idea of how this works
You will find that the library keeps track of which items have been synced already by storing them in different keys/properties, depending on sync/caching status (local vs. common vs. remote). And thus, if it sees the remote not having an item anymore, it considers it as having been deleted from the remote. Which will also delete it from the local database.
I think this is the part of the sync where that happens:
(The return value there is used by other code to update the cache.)