We recently had to move from the iTMSTransporter app to atool, because Xcode 14 removed the former. We immediately hit an issue that's very similar to what's been discussed in this thread.
For example, if there's a release train 1.10.0, and there's already a build with build number 12345, one can't upload a build with number 1, 2, ... all the way up to 12345. Given that it used to work with the iTMSTransporter app, it seems like a limitation on the atool side.
HorsePferd
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