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The integration of generative artificial intelligence into clinical documentation workflows promises substantial efficiency gains yet introduces persistent misalignment between AI-generated drafts and individual clinician judgment. This conceptual systems research article advances a novel human-in-the-loop adaptation theory that explicitly models clinician preferences as dynamic, context-sensitive inputs rather than static constraints. Drawing on peer-reviewed evidence, the manuscript synthesizes how preference elicitation, real-time adaptation, and closed-loop governance can transform AI-assisted drafting from a supplementary tool into a co-evolutionary clinical intelligence infrastructure.Central to the contribution is the introduction of the clinician preference orchestration and adaptation framework (CPOAF), a layered architectural model featuring four interdependent strata and a star-topology feedback mechanism that propagates preference drift signals radially from peripheral clinician nodes to a central orchestration engine. Three interpretive mathematical constructs—decision confidence, monitoring burden, and drift sensitivity—are formalized to guide theoretical deployment without empirical benchmarking.The framework addresses governance constraints, data-modality specificity, and deployment-environment heterogeneity while preserving clinician autonomy. By foregrounding preference modeling as the core adaptive mechanism, CPOAF offers a scalable infrastructural blueprint for next-generation AI-assisted drafting systems that remain clinically grounded, ethically defensible, and institutionally sustainable. Implications extend to health-system informatics, regulatory science, and human-centered AI design.