One of my installs recorded that the 2.3.9 delete files cleanup step failed. Anybody happen to have that list handy of which files get deleted as part of the 2.3.9 upgrade?
check that your ftp user is the same as your server user.
in my case, i made a manual file edit via ftp as me@mydomain.com ftp account, and then when you 1 click upgrade, it sets the files to nginx as the owner, for example.
in my case, it was the JS hotfix for image rotation. just chown that file back to niginx instead of me@.