I have seen FM do weird things when you make one connection by IPv4 and then try an IPv6 from the same client to the same file., but this is likely not the issue. Did you speak with the Apple directly about the exact issue. It takes time t get through to someone in developer support, but they try to help the best they can.
I would suggest you use a FQDN in your external data source entry with proper DNS entry to route to your IPv6 server. This is better on many levels. You get SSL for the FQDN (secure and progressive DL for mobile) and a change in server is a DNS entry instead of trying to make sure every user updates with a new IP address entry in the file.
Apple has been pushing IPv6 app compatibility for a while now and for the AppStore it is a requirement to be compatible. Supporting IPv6-only Networks - Support - Apple Developer The IPv4 data source entry may be causing your issue.
Ok, i will try a new submission with the FQDN.
See how that goes.
Thanks for your suggestion.