The option to clear Recent Files works to clear the list only for the current session. When Notepad++ is reopened the same files are listed again.
Another problem seems to be hiding in that same functionality. Some new files are not replacing old files in the list. That is, on some occasions when I edit a file and save it, upon starting Notepad++ again the latest file may not be listed, but numerous files I have not used recently are still listed.
The Recent files (sub)menu lists closed recent files most recently used. So, if a recent file is currently opened, the menu won't list it.
Does the same issue arise when you add a new search pattern? Both are stored in config.xml: if N++ cannot write to that file due to a permission bug, oops Windows security enhancement, then you may observe this. So please check your config.xml file(s).
By installing outside of C:\Program Files, I have always avoided these problems. See if that makes a change for you.
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