It appears to be an error on Apple's side.
Here is an ugly workaround:
Increment the version number as well as the build number, then upload.
Incrementing the version in addition to the build number will have to be done for every build that is uploaded until the issue is fixed.
Floating Wrench
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I have an application that uses bonjour server advertising as well as direct local IP URL requests (to Hue bridge).
After updating to Sequoia, the app runs in Xcode 16 and displays the network permission popup and can access the network.
When distributing a compiled build to the same machine with Developer ID (notarized or not), the network permissions popup is not displayed and the advertised services are not available on the network.
In Settings -> Privacy & Security -> Local Network, there are two toggles with the same app label. When one is toggled the other changes as well.
Any suggestions?
Have there been any applicable updates to the FAQ for Local Network Privacy specifically for macOS that I may have missed?