Uhh...

I agree, this is a bug. I have this in todo (at least using appdata directory as MS recommends), but was doing other things, because nobody was complaining

)
Thanks for deep analysis

I think I would not change this for 1.4x branch, but probably for 1.50.
The installer needs to tell the user when it renames their customized syntaxes to .old etc. and where to find these files so they can merge in their customizations to the new files.
... installer does not know, that
user has modified files, it only knows that they exist. It does not parse xmls, and there is also no version inside of the xml...
What I can do (Arthur has suggested some when) is flag in installer, which can disable overwrite of defaults.
Another thing, is to find out all settings that user wants to have different from defaults and move them to user_xxx.xml files (as file extensions for example).
Best regards,
Alex.