I just figured out why my OneDrive folders were being so weird. If you select multiple files, right-click and pick "keep on this device" it doesn't set that flag, it toggles them. So the ones that already had that selected are now deselected. This even works iteratively for folders. I have a bunch of files with "keep on this device" selected. If I go up a folder and check "keep on this device" for the folder they're in the status of all of the files within that folder get toggled rather than set correctly. This is for my OneDrive for business stuff. Haven't tested it with personal OneDrive yet. This is easy to work around once I figured out what was going on.
I'm using DO version 13.23 x64 build 9483 on Windows 11 Pro 25H2 26200.7840