you must add one attribute to language xml file
i.e. if you want to change language czech to RTL, then you must edit file czech.xml in c:\Program Files\Notepad++\localization\ directory (it is the location, where the notepad++ was installed).
Then you must find tag Native-Langue and add attritube RTL="yes" to it.
i.e. before change:
<Native-Langue name = "Čeština" filename="czech.xml" version="6.6.8">
after change:
<Native-Langue name = "Čeština" RTL="yes" filename="czech.xml" version="6.6.8">
then only restart Notepad++.
Here is link to the official manual with brief description