After discussion on T164975, it turns out that ar_timestamp column in archive table is not suitable for indexing deletes, as the timestamp is when revision was created, not when revision was deleted.
Looks like instead, we need to use something like:
SELECT log_timestamp,log_namespace,log_title,log_page FROM `logging` WHERE (log_timestamp >= '20170101000000') AND (log_timestamp <= '20170828201852') AND log_type = 'delete' AND log_action = 'delete' AND (EXISTS(select * from archive where ar_title = log_title and ar_namespace = log_namespace)) ORDER BY log_timestamp ASC
We've stopped using log table after the fix to T54612, but look like we still need timestamps from there.