apt-get autoremove wants to remove 1000+ packages and everything

It lists 1546 packages to be removed. Including xorg, xserver and other core packages. I entered "yes" in the past and as expected it bricked the OS I had to reinstall it from scratch. This time I answered "no" and tried:

sudo apt-get -y update --fix-missing

but it still wants to remove everything. How can I fix that please!

This happens most commonly when folks bolt a Desktop onto a Minimal install. But it can happen when you bolt ANY kind of major stack onto an Ubuntu system.

In the Desktop example, it means the entire desktop stack is hanging on a single metapackage (like the ubuntu-desktop package). When you remove some element or application of the Desktop --which removes the desktop metapackage-- that action makes the whole desktop stack eligible for autoremoval.

Prevention

• When folks use the real Desktop Installer, there's an additional layer of apt-marking protection to prevent folks from autoremoving their whole desktop.

• You can also explicitly install (or apt-mark) the applications you use. That way, most of your desktop dependencies won't be auto-removed.

  sudo apt install shotwell         # Example of explicitly installing
  sudo apt-mark manual shotwell     # Example of apt-marking
  

• install using Task Packages, for example Ubuntu MATE is installable by

  sudo apt-get install ubuntu-mate-desktop^
  

  Note the ^, it means task; installing this way will prevent ruining the system if someone wants to run potentially dangerous commands like sudo apt autopurge ubuntu-mate-desktop for meta-package.

Recovery

• You can simply re-install the desktop task package.

  sudo apt install --reinstall ubuntu-desktop^ # Example of re-installing a Ubuntu desktop task
  

• You can also copy the long list of removals and paste that list into an install command. Note that naming a package makes it ineligible for future autoremovals, but your concern seems to be too many autoremovals instead of too few. If you need to recover that list, it's in your /var/log/apt/history.log file.

If you think autoremove is removing things you want to keep, for each package you should:

• use dpkg -l | grep $shortpackagename to check if there is a newer version also installed, in which case it is ok to remove the older one
• use apt rdepends $packagename to see if there is a parent package that you also want. If there is, install that parent package or a reverse dependency of that parent
• If there is no (obvious) parent dependency package you want to keep, but you still want to keep it, apt install $packagename so it doesn't get uninstalled by autoremove.

A good example of the above (as mentioned in comments), if autoremove wants to remove xorg then install ubuntu-desktop and you will probably find that many of the autoremoves will now have a parent dependency installed and the list will get shorter.

Once the list is short enough that what is left is either obsolete packages or things you are sure you don't care about, then autoremove is safe.

This situation is not normal, it doesn't happen automatically, It is caused by, at some point, something critical being removed from the system that causes some important parent package (like ubuntu-desktop) to be removed.