If the values are already loaded (which happens when the package is installed) then you have to change the values via acs-lang (most likely mounted at /acs-lang/admin/) thru your browser.
For example. Going to:
/acs-lang/admin/edit-localized-message?package%5fkey=acs-subsite&locale=en_US&message%5fkey=email_body_Forgotten_password
Will allow you to edit the English message for email_body_Forgotten_password for acs-subsite
Either that, or I believe clicking on "Import all messages" from /acs-lang/admin/ will re-load your catalogs from file.
