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In my last job.
My Company did not file site-specific SOPs in the sponsor TMF. They should remain at the site and be available upon request as part of site selection, or during an audit or an inspection. Other organizations, maintain one TMF set Per site to maintain site-level documents, so we could technically place the site-specifics SOPs within 01.01.04 if situation arises.
Your organization should have a SOP for preparation and maintenance for TMF.
hope this helps!