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I believe this is an issue we cannot fix, what is happening is the new content definition comes down to client, it now sees the old value and thinks it's a manual edit which must be preserved, there's no way for us to know it was from some since removed sku override.
Has to be worked around manually if this is hit, just edit the value, remove the content set, add a system override for it, etc. Regeneration of the file or re-adding that content set should fix the issue.