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The team said that .msix package submissions work just like appx packages which means if you submitted an appxbundle all future submissions for that app would need to support the appxbundle.
And from this document- Resolve submission errors, ' Be sure that you follow the steps in Package a UWP app with Visual Studio when creating your app's package file, and only upload the .msixupload or .appxupload file on the Packages page of the submission, not a .msix/appx or .msixbundle/appxbundle.'
The team already knows your issue after I reported this. Please open a support ticket for this here: Contact Us. Choose to Contact us, select Dashboard for Topic and select App submissions for issue type and Package Management for subcategory. You could get more help with the account issue via the ticket. So that the team could talk to you directly about this issue.