You can use each of the above commands individually or together. There is not much of anything happens in between.
The command 'sudo apt clean' will not lose valuable files.
The command 'sudo apt autoremove' is generally safe... But Always Read Terminal Output before hitting "y" key or (yes).
I cannot stress this enough: Always Read The Terminal Output before making a decision.
"Autoremove" removes automatically installed files. For example, if you 'sudo apt install gimp', it will install other necessary files for gimp along with the base gimp program. These are auto-installed.
You can mark any package you want to "manually installed" to prevent them ever being autoremoved. You can do this simply by trying to install it with APT even though it is already installed. For example, with gimp, it is installed - and you enter in 'sudo apt install gimp', the terminal will say, "gimp is already the latest version. Set to manually installed."
The other method of preventing autoremoval on a package is with apt-mark as covered in another thread.
sudo apt-mark manual (package-name)
Ref: Finding package name: