@alexandratepp

If, when you login to the CLI as root or a sudo user, you’re unable to view the folder, it doesn’t exist. The root user has the highest allowed permissions and the sudo user is allowed to utilize those permissions when sudo is called, thus giving the sudo uses the same permissions for the duration of the command. If either or both fail to see a folder, it simply does not exist on the system (unless there’s something majorly wrong with the current permissions - i.e. something has really messed things up).

As for logging in as root, you should still be able to execute su - to escalate. Simply because you’ve disabled root login doesn’t mean that you can’t regain access :-).

That said, ideally, for security, you should (as you’ve done) disable root login, though you should also create two additional users in the following format:

a). A sudo user, which you’ve done.
b). A new user for each account/domain.

The sudo user is who you login as when you need to perform escalated commands (i.e. updates, upgrades, package installation etc). The “new” user, which is associated with a specific account or domain is who should “own” the directories, files etc - this is also who you should be logging in to SFTP with.

This user should not have any sort of escalated permissions, only the basics that allow them to read, write and execute from directories and/or files they own (thus preventing one user from being able to read, write and execute another users files or from their directories).

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That said, what would appear to be the case here is that while you’re being led to believe that a theme or file is uploaded, it’s not, otherwise you’d be able to see it at the very least. This boils down to permissions and the fact that the user that is actually handling the uploading does not have permissions to write to the directories in your home directory.

If we take a basic directory structure such as:

/home/domains/yourdomain.ext/htdocs/public_html

Then:

/home/domains

… should be owned by root and:

/home/domains/yourdomain.ext

… and all directories & files below it should be owned by user where user = the user of your choice - i.e:

/home/domains/yourdomain.ext/....
/home/domains/yourdomain.ext/htdocs/....
/home/domains/yourdomain.ext/public_html/....

… where .... would be files & directories.