I also have the same issue, do you have any fresh information ?
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After checking on real devices: iPhone on iOS17 and Apple Watch run-in watchOS 9, I confirm that App Store don't install the new version if both minimum OS requirements are not met.
So it's handled perfectly well.
I also have the same question.
It seems the migration is never called.
Yes !
And it's working perfectly !
I have exactly the same issue with a workout app and its iPhone companion app.
HealthKit seems to be out of sync, it's like we have 2 different app reading and writing in 2 different HealthKit stores.
I haven't found any documentation on that ...