Same thing happened here and it took me a while to figure out the cause of this issue. Very frustrating.
My current workaround is to add the command for automatically resolving the dependencies immediately after bumping the build number, as follows:
cd "${PROJECT_DIR}" && agvtool bump && xcodebuild -resolvePackageDependencies
Would love for this to be fixed soon or the letting us know the reason behind it if this is an intended behavior.
zhang13
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Same here on Xcode 14 beta 6 / iOS 16.0 beta 8. Would love to know if any updates.