How to migrate Notepad++ settings?

I found the configuration files under
%appdata%\Notepad++.

Many settings in NP++ can be automatically kept in sync (and migrated) between multiple instances by using Settings > Preferences > Cloud

The first time you set a cloud location (which can just be any folder path), it'll backup your current settings into that folder and then draw from there going forward. When setting the cloud location on a new machine, it'll read in those files there.

The cloud settings consists of the following items:

^{Note: You might need to remove the existing files with the same name under %appdata%\Notepad++. in order for the cloud storage files to take priority}

You have already found the full list of Notepad++'s configuration files. If I were you, first I would copy the whole Notepad++ folder under the Program Files, and save it for some time. Then I'd start to use all the files listed on the NPP page, and after making sure everything's OK, I'd delete the backup.