Hi,
Thank you for the details!
They ARE in the media library if you expose hidden files.
This might be related to the issue. WordPress does not have an option to expose hidden media files – at least I am not aware of such thing. The files may not actually be in the media library, it might be only an addition by a plugin to show them there.
If you are using the index table engine, make sure to re-create the index. If the files are in the library, it will pick them up.