LogCook: Error: Content is missing from cook. Source package referenced an object in target package but the target package was marked NeverCook or is not cookable for the target platform.

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I also have this problem in 5.4.1. I made a copy of my 5.2 project (which packages fine), tried to package, and I get about ~200 of the “Content is missing from cook” errors that look similar to this:

UATHelper: Packaging (Windows): LogCook: Error: Content is missing from cook. Source package referenced an object in target package but the object was stripped out of the target package when saved.
UATHelper: Packaging (Windows):    Source package: /Game/Blueprints/Story/StoryInteractable_Core_MistVault
UATHelper: Packaging (Windows):    Target package: /Game/Blueprints/Story/StoryInteractable_Core
UATHelper: Packaging (Windows):    Referenced object: /Game/Blueprints/Story/StoryInteractable_Core.StoryInteractable_Core_C:BlockerCapsule_GEN_VARIABLE
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