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This does not look like something that changing the model or simply splitting the SharePoint site into more knowledge sources will necessarily solve.
There are actually two different SharePoint retrieval paths in Copilot Studio. The full SharePoint knowledge source queries SharePoint search at runtime, whereas Upload files > SharePoint stores and vector-indexes selected files/folders in Dataverse. For a curated document set, I would test the latter and compare the response time. Microsoft documents the runtime differences here:
https://learn.microsoft.com/en-us/microsoft-copilot-studio/knowledge-unstructured-data
If you need to keep the full SharePoint integration, Microsoft also specifically recommends using the SharePoint knowledge-source Advanced settings filters (Title, Author, Modified by/date) to reduce the search scope and improve performance:
https://learn.microsoft.com/en-us/microsoft-copilot-studio/knowledge-add-sharepoint#filter-your-sharepoint-source
I would also avoid the GitHub Copilot harness for this particular test. Microsoft positions that harness for reasoning-heavy, multi-step work, while the Standard harness is intended for predictable Q&A/help-desk scenarios using enterprise knowledge:
https://learn.microsoft.com/en-us/microsoft-copilot-studio/harnesses-overview
So I would benchmark the same question with: Standard harness + one tightly scoped SharePoint source, then Standard harness + SharePoint files/folder indexed in Dataverse.
If the minimal configuration still consistently takes 40–60 seconds, I would raise a Microsoft support case rather than continue restructuring the SharePoint site. At that point the latency is likely in the Copilot Studio/SharePoint retrieval pipeline rather than in the agent instructions or model selection.
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