Hi,
1. As I have said in that previous reply, you can add temporary FTP access, if you want, I can check why ACF is not returning the missing values there. If there assigned items, it should be returned.
2. Unfortunately there is no way to do that. Repeater/object storage fields are not officially supported for filtering. We tried many different ways to get around them, but there is too much flexibility on how those fields work, and there is no good solution for it.