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Sorted out. The answer was inconsistency between all Provisioning Profiles for that bundle id. We regenerated all provisioning profiles when we removed AppClips (Development and AdHoc) but not AppStore. That was the culprit. It's really weird to keep signing an app with a Provisioning Profile that included com.apple.developer.associated-appclip-app-identifiers, but we don't have that on entitlements anymore on the app (on our AppStore builds). So, to be safe, we deleted all Provisioning Profiles on Dev Portal and regenerated them again, and it fixed the issue. Make sure you don't have any AppClip app id created on Portal, otherwise the Provisioning Profiles you create for the parent bundle id will always include com.apple.developer.associated-appclip-app-identifiers.

After inspecting our AppStore Provisiong Profile I can say that I’m seeing the two appids there, inside com.apple.developer.associated-appclip-app-identifiers. So that’s why we didn’t have issues with the Archive/distribute for AppStore, but I’m worried that as soon as we renew the provisioning profile, we cannot distribute due to this issue that is only happening right now for Development and AdHoc. Not sure if it’s relevant, but we still have both app IDs in our Apple App Site Association file. Could that be the issue?