Some indication from Balsamic discussion that we are not handling all queries for the second of the two mirror instances of BNDs in particular.
On a quick read, I saw no ordering of either intra- or interchrom coords for queries (note similar recent change for svdb) on query, as would be expected for storage. But, clients may be aware: let's make a some simple tests, perhaps all is still well, but at least we should document this.