The fundamental difference between Windows and Linux: developers believe Windows is the user (even admin) stupid system (I think, statistically, they are right), the developers of Lin - smarter (which is probably also consistent with statistics). So when you run the command from under the root, clearly understand what the consequences will happen.
I have so much there set up, is there a way to reinstall the image but keep the data ( configs in etc, home folder etc )?
I doubt that you have configured something harder than Nginx+php-fpm+mail+mysql+certificates+ssh. An experienced admin will do it for half an hour, fifteen minutes of which he will have to work automatic deployment scripts (or five minutes if the server is smart).
Maybe you can disable the system in Linux, I do not fully understand how I, for example, to upload files to a folder wget'ohms and edit via ftp. I can somehow user FTP add in root group?
Impossible. Even if such a possibility existed. It bothers you because you don't know her. A properly configured system does not require constant change and operates transparently, helping you to maintain the level of security at the proper level.
Specifically, your problem with the access: read about users and groups in Linux.
For your situation: don't do anything yourself! Hire an administrator, who will deploy the new system and will transfer information correctly, it won't be expensive, I'm sure. Pay money and get a properly configured system, and a bonus, a good introduction to devops is the right investment in your development.
For the future:
- do not use FTP
- read the documentation
- experiment on a virtual machine