Ok, it’s been awhile but this has happened before. If I recall, the issue was the webhost kept deleting the file. They were doing for the user’s “safety”. The webhost had a script or something running which would delete anything that was able to recursively delete files. The
class.filesystem.php has this ability so it can delete the images and their cached variations when an entry is deleted. The solution was the webhost had to whitelist the file just like they whitelisted WP files that can recursively delete files too.
Hope that helps!