"what I should see in the website's control panel File Manager"
What are you using to look at the site? By that I mean what software - are you looking via Net Objects Fusion, or something else?
I've taken a look at your server files, and I can see that all your site page files have been updated today. You say that there has been a latest, single change, but you've obviously re-published the entire site today, and I'm wondering why you did that - Why don't you tell NOF just to publish the pages that have changed? It's a much faster way of working.
Looking at the server via WSFTP Pro, which is my preferred FTP program I can see your site looking exactly as it should for a site that's been designed in NOF. That's the way you should keep it - keep telling NOF to publish everything to the public_html directory, and all will be well.