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We have tested an update using an explicit app id and did not run into an issue. Our next step is step up one as close to yours as possible. To do that can you send us a screen shot of your app id settings in the developer portal. Please send it to support at genuitec dot com
I don’t think just the IPA file will really help. If your are willing to give us temporary access to your account we can try to upload the file for you and see if the same error comes up on our system setup. If this is possible you can send the IPA and info to support at genuitec dot com. Please include the required Application information so we can upload with Application Uploader.
I was able to successfully update both apps you sent me without issue. If you have not tried it my suggestion is trying to completely uninstall both xCode and Application loader, restart and then reinstall them.