Ok, i've confirmed this is a new problem introduced in Transporter 1.3 (1380). I was able to upload the same .ipa via fastlane with no problems. Still crickets from Apple support. The developper program is a joke.
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I'm having the same problem. iOS only app. Has been uploading fine with Transporter for over a year, and now it's not allowing to upload. I don't use Xcode so i don't have any alternatice. I've reached out to Apple support, but have not heard back yet.