While hypergraph-based Retrieval-Augmented Generation (RAG) effectively captures higher-order multi-entity correlations, existing paradigms treat extracted hyperedges as isolated factual assertions. This structural fragmentation engenders rigid "knowledge islands" that bottleneck multi-hop causal inference, temporal tracking, and narrative synthesis. To systematically address these challenges, we introduce Dual-Hypergraph Indexing (DHI), a hierarchical representation framework that elevates discrete facts into structured analytical insights. DHI couples a foundational entity-relation factual hypergraph ($H_K$) with an elevated deep-insight hypergraph ($H_D$) via a dual-pathway aggregation algorithm. Specifically, DHI employs: (1) importance-driven hub aggregation via 5-metric topological profiling and adaptive thresholding to capture spatial semantic clusters; and (2) temporal chunk-chain progressive aggregation via sliding-window greedy exploration to track chronological evolutions. Across five benchmarks, DHI achieves state-of-the-art performance, boosting logical coherence by +1.53 on the multidisciplinary Mix benchmark and scoring 85.78\% on complex medical pathology reasoning tasks. DHI provides a robust architecture for next-generation multi-hop RAG.

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