File manager from cpanel is not showing all files

Accessing the cpanel is not a problem here, and file manager is working fine.
What isn’t working is the files I’m looking for.

What I’ve done so far is,
created a website and loaded a backedup file from “All in one wp migrate” plugin.
Now I’ve a different theme running on my website, different plugins and other stuff. This is not showing in my file manager but a simple vanilla wordpress install.
This is my website link if you want to lookup. Markhor Studio - an internet company from Pakistan.

If you disable Cloudflare does the issue persist? Have you tried clearing the cache?

Disabling doesn’t work and clearing cache either.
By viewing the page source I’m able to find that it is pointing to same theme I’m using like, etc, but not accessible via file manager.

here is the screenshot of my theme directory:

Any other help?

Sounds like the tool you’re using to browse is pointed at the wrong directory. You may want to contact the sysadmin for the server or attempt to connect via FTP or SSH and browse to the files directly to confirm the location they are being served from.

Changing the directory can create a conflict?

If it’s the wrong directory? Not a conflict, simply looking at the wrong data. Where are the files located on the machine that your webserver is serving and where is the browser pointing? Doesn’t sound like they are the same place.

If I browse /var/www/html/ for files which are actually located in /var/www//mydomain then the files won’t be the same. You are showing a screenshot of a theme directory, but there’s no indication that it is the theme directory and based on what you’ve said so far the evidence points to it not being the theme directory for the website in question.

So, I think I have found the directory. What if I simple cut and paste in to the .com/content ??