Update removed my software

Hello.

Installed fresh Calculate, than installed Lazarus, Terminator, something else.
When I run Software update updater noticed that it will remove “unused” software
and removed Lazarus and Terminator. I installed it again, not a big deal,
but just want to understand how it’s possible that updater remove manually installed software
because it’s “unused” and how to prevent it?
Was it removed because I perhaps have never ran it after installation?
What is the logic for updater to check used/unused software?