When Tools->Configuration Files ... is used to edit a config file it is copied in its entirety to the buffer, so when it is saved it overrides all the settings in the system filetype file, not just the ones that the user changes. So system filetype files distributed with new versions of Geany will be ignored.

Suggest when the file is loaded into the buffer it be prefixed by # to make all contents comments, so the user only need uncomment those they edit and so only those entries will override new system files.