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Do you have a folder with more than 100,000 items inside of it?
(files, other folders, shortcuts, etc.)

In SharePoint, once a folder contains more than 100,000 items, the folder permissions cannot be modified. This means that individual access cannot be granted nor removed from the folder until it contains fewer than 100,000 items.

To alter access while the folder has more than 100,000 items, you must use User Groups. Learn more: Manage Folder Permissions in SharePoint using User Groups

Do you have a large number of files in a historical, or archival, status (300,000 or more)?

(Records Files that you are keeping but do not access frequentlyin your normal, day-to-day work)

You may want to have this data reside on a discrete SharePoint site. Learn more: Archival SharePoint Sites