Restore a backed up project - Prefab Connections

(For TLDR please jump to last section where my questions are.)

I tried to restore one of my backed up projects (just in case of a hazard scenario.)

I was backing up (copying the folder) Assets, ProjectSettings, UnityPackageManager just these three folders. I also have some rare full folder backups but I thought these 3 folders are enough. (Also I recall that I was able to restore just using these 3 folders.)

But today when i restore, first I got "Namespace not found" error. One or two classes were unreachable at visual studio. Somehow I could get rid of it.(Still don't know how. Deleted the VS project files. After the deletion the errors were still present. But now they're gone.)

But the Prefab connections were also gone (from the start). So my questions are:

1. Is there any way to restore the prefab connections in this scenario(Restoring a project with only Assets, ProjectSettings, UnityPackageManager folders) or should I connect them manually again?

2. Apart from Prefab Connections, everything should be fine? (I will also test it now, but believe in your guys' experience and knowledge more than my quick test as I can miss something. There are a lot of attributes and settings in a project as you already know)

3. In which file does prefab connections are kept?

4. What is the proper way of backing up a Unity project in case of a recovery situation? Is copying the whole folder enough? Was copying these 3 folders a mistake? (Assets, ProjectSettings, UnityPackageManager)