We're having a somewhat similar issue where we upload two builds (two variants of our app with different bundle ids), one gets associated with the wrong app and the other disappears completely. We get an error email about the first (that gets associated with the wrong app) but nothing about the second. Also using beta 7.

This is fixed in iPadOS 16 beta 11 and iOS 16.1 beta 4

Did you find a solution to this? I am getting the same error code in a similar circumstance.