Since Notepad++ Portable 8.1.1 up to the latest version (8.1 is the last correctly working version), on a Windows 10 x64 system, the program doesn't actually use any .xml files from /Data/Config besides session.xml. On fresh install and first run,
are created in Data/Config. From these only the plugins directory (and its contents) and session.xml are moved to application directory (App/Notepad++64 on x64) on start and written to & moved back on close as intended. All other configs are saved anew by the program (because they didn't exist in the app directory) and reside there permanently, even after the app is closed, to the point that everything except plugins dir and session.xml can be deleted from Data/Config with no effect (it won't be recreated either). Another consequence of this is since userDefineLangs directory is created only in Data/Config, and not moved to application directory, notepad++ doesn't see any UDL schemes, e.g. for markdown.
Could you please take a look at it when you get the chance?