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So don't worry so much about how to use  had had  as a unit of grammar, they will come together naturally when you want to express the verb ' to have ' in the past perfect. Let's consider a different verb for a moment like  to want .
When two or more consonants, often of a similar nature, come together, there is a tendency in English to simplify such a cluster by eliding one of them. The longer the cluster, the more of a chance there is of elision occurring.