This study investigates how document structure and preprocessing strategies influence the performance of Retrieval-Augmented Generation (RAG) pipelines in domain-specific question answering, using university curriculum handbooks as a case study. We evaluate multiple data representations, varying in chunking method, punctuation level, and structural format (HTML, plain text, JSON), within a privacy-preserving pipeline that combines semantic vector indexing with a lightweight, locally deployed LLM. A benchmark of curriculum-related queries, covering both simple lookups and multi-hop reasoning, was used to assess performance under controlled retrieval conditions. Results show that semantically coherent chunking, manual or LangChain-based, substantially improves accuracy, with gains exceeding 25% points for medium-difficulty queries, while structurally dense formats like raw HTML or JSON reduce performance. Fixed-effects modelling confirms chunking and natural-language rephrasing as significant positive predictors of correctness, whereas punctuation density and markup type show no measurable effect. These findings highlight the critical, yet often underexamined, role of input data structure in applied RAG pipelines for curriculum advising, where accurate retrieval is essential for tasks such as prerequisite checking, program planning, and subject eligibility. The study presents a reproducible framework for evaluating preprocessing decisions in academic QA systems. This supports the development of reliable, privacy-compliant advising tools.