Something like:

entity.Where(x => x.JsonCollection[0].NestedReference.Name != "Foo")

When done in projection, this breaks the ordinal key logic, so we need to force AsNoTracking for these queries.

We could maybe utilize json de-duplication logic when the owner is present. For now de-dup is only working on navigation names, would need to incorporate array indexes also.

i.e.

entity.Select(x => new { x, ArrayAccess = x.JsonCollection[0] })