Per default, merging (overwriting existing property values + adding missing ones) of INI files is disabled.
BUt you can enable it for specific INI files inside your ja2.ini.

Just put the property "MERGE_INI_FILES" in your ja2.ini.

For example, if you want to enable merging for the files "Ja2_Options.ini" and "Ja2Settings.ini" just enter
the following line in your ja2.ini file:

MERGE_INI_FILES = Ja2_Options.ini, Ja2Settings.ini

Now you can put your custom Ja2_Options.ini and Ja2Settings.ini inside your
"Profiles\UserProfile_JA2113" folder. Please note, you only need to put the custom properties (that differ from the base 1.13 INI) plus the section name
inside your custom INI-Files. That's all.