If you have a look at Preferences -> General you will notice at the bottom of the panel, there is a setting Load preferences from a custom folder or URL:. There is a button next to it Save settings to Folder.
So all you need to do is save your settings first and load it after you reinstalled your OS.
If the Save settings to Folder is disabled, select a folder (e.g. empty) in the Load preferences from a custom folder or URL: text box.
In iTerm2 3.3 on OSX the sequence is: iTerm2 menu, Preferences, General tab, Preferences subtab