Hidden files automatically deleted locally

The following happened to me …
I synchronized my /home/$USER in the desktop app for Linux, when I was synchronizing I went to sync settings and unchecked hidden folders (with a dot in front). However, my entire home was already synchronized on the cloud, so I removed the hidden files from there and deleted the trash. Even if I deselect not to synchronize these hidden files on my local machine, they have all been deleted. I am now trying to restore a bkp and try to recover.

What is the correct way for me to set to sync all of my /home/$USER and not just sync the hidden files that are in my user’s main directory?