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Hi,
IMHO, the easiest method is to rebuild the server with an existing snapshot on DigitalOcean if you have one.
If not, manually fix it by following HERE for the WordPress official recommended fix method.
If you already have any of malware scanners, just try it.
Note, you can only upgrade from CentOS to CloudLinux, not for Ubuntu/Debian system.
I hope you get to the bottom of this.
Best, Eric