What is deleted during a macOS reinstall?
In the past - Apple had three methods to install:


erase and install (now deprecated)
archive + install + migrate
upgrade install (now deprecated)


Now, when you run the installer - it is always archive, install, migrate. SO the existing system folder isn't touched (it gets archived) and a new system folder and library are created on the drive.

So some folders get erased entirely, some have modification scripts and most user folders don't change. The user folders might get a light script run to clean known issues, but in general - the things in the user home folder are left alone.

The system then reboots into the newly functioning system to run further installations and then kicks off the migration script. That script is responsible for the infamous "about a second" step where it actually goes over each user folder and migrates all the apps, settings and checks for known incompatible software and packages so they can be disabled before any user logs in to the newly made system. The whole process usually takes 5 to 25 minutes for the system tasks and then the last user step can take a few moments or a few hours in my experience. Past an hour, it is usually hung and you might need to do an erase / migration from backup.


How long can I expect my system to be unusable during an upgrade to OS X Lion?


The old system is then deleted unless the script detects a potential that it will be needed or the migration failed in some manner.

I you wan to do an erase instal, you need to erase the drive using internet recovery, target disk mode or similar and then run an installer on a blank volume.