Check the project folder permissions, I did a little test by removing write permissions and deleting a folder in the unity project it comes back as the editor can not delete the folder.
Wich folder? I can delete files directly by browser and “mc”.
target SSD have HPFS/NTFS type and mounted by root with drwxrwxrwx permissions
/dev/disk/by-uuid/706CA29207D5FCC0 /media/disk2 auto nosuid,nodev,nofail,x-gvfs-show 0 0
These are important details to mention when reporting bugs.
We’ll investigate with a similar setup. Meanwhile, you may be able to work around by using a copy of your project on a more common filesystem (e.g. ext or xfs).