Start with a narrow collection
I would begin with a collection that has a clear owner and a known permission model, such as approved internal templates. Ingesting the entire document management system creates a permissions project, a records project, and a search project at once. A smaller collection makes it possible to establish whether the controls actually work.
For each document, record its source identifier, version, owner, permitted groups, current status, and last successful permission refresh. Keep that metadata with every searchable chunk. Splitting a document into smaller pieces must not detach a paragraph from the restrictions that apply to its parent.
Make collection membership explicit. A file appearing in a convenient shared folder does not establish that it belongs in a firm-wide knowledge base. Someone with responsibility for that material should approve its inclusion. A rejected or retired template should disappear from ordinary results while its records lifecycle remains governed separately.