Users need to select from generated / uploaded files — however some folders/files are ineligible for selection

A major part of our product is the data room. Users generate and upload up to hundreds of documents. In various workflows that require company approvals, they can pick from documents in the data room rather than uploading a document.

However only certain documents in their data room should be selectable. For example if the workflow asks for a Board Approval, the user should only be able to select from board approvals or from one of the documents they uploaded (because we don't know what they are). So most of the documents and folders in their data room shouldn't be selectable.

Right now we show a filtered list of documents and folders - however recently we've gotten feedback that users are confused when they don't see documents they know they uploaded/generated.

How do we highlight what is applicable, reassure users that the file structure/everything is still there, but also avoid clogging up the selection with non-applicable files?