The behavior you are seeing is by default. SQL Deletion Policy deletes full index documents based on their document Key, not specific fields. The policy doesn't have a way to know the index has values from other sources too. If there is a combined index and you would like the behavior you are looking for, you may try instead using a Logic App SQL trigger to update only specific fields with Add, update or delete documents, instead of the Deletion Policy.
I have shared the answer posted by Gia Mondragon - MSFT (from Search product team) from your discussion thread to benefit the community.
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