I have not experienced this when upgrading NPP via the Upgrade Notepad++ in the Help (? ) menu. I thought I hadn’t customized the stylers at all, but when I looked, I had changed the font a long time ago (probably sometime early in version 6). I also had to look at what is in config.xml, and I would notice if my recent file list were cleared! I’m not sure if the Wiki is current, but as of v5.4.1, at least the stylers and langs files are not touched.
This page also mentions that
When it looks like a setting is lost, a common cause is that there are two sets of files, one in the %APPDATA%\Notepad++ folder and one alongside Notepad++.exe. Then either N++ doesn’t read the right file, or the setting was saved into the wrong file.
Regarding an export of settings, there is an issue on GitHub that discusses it. However, that issue is closed. I left some comments on it, but the issue has been raised and closed before.