Duplicate files in Program Files and in %APPDATA%
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I’ve been banging my head against a wall because I could not get the function list to work when I was trying to add VB support. I finally found the suggestion to delete the copy in %APPDATA% and lo, it works.
My question is, what is the purpose of having files duplicated there?
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In %APPDATA% every user has own setting and can change them individually. You will not waste your time if you read https://npp-user-manual.org/ before:)
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Which one is in effect is controlled by the
doLocalConf.xmlfile:- 
If the zero-length doLocalConf.xml file EXISTS in the same folder as notepad++.exe, then the other xml configuration files (e.g. function list) in that same folders will be used
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If the zero-length doLocalConf.xml file DOES NOT exist in the same folder as notepad++.exe, then the xml configuration files (e.g. function list) in %APPDATA% area for Notepad++ will be used
 
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… And if the Cloud preference is enabled, then some (but not all) of the config files will be read from the Cloud directory instead of AppData or the executable’s folder
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Thanks to all three of you. I understand the reasoning now.