Ah, that makes sense. I've never added an index myself, but essentialy Datomic has to rewrite the main index tree. In other words, all of the stored data, since there is no data stored outside of the covering indies. So I wouldn't be surpised if that causes some down time if you have lots of data in your database.

I think "late indexing" maybe referring to an implementation detail. The indexes aren't updated after each transaction. When you query the db, the result is a merge between the index and the transactions that haven't been indexed yet. The index is updated in batches.