All changes regarding Z39.50 targets, collections, collection strength etc, are stored in a MySQL database. You can change the content by using the TLDD admin interface or use a generic MySQL tool such as phpMyAdmin.
The admin interface is located in lot/admin/.
All information about the targets for the search interface, are stored in a cached file, in order to increase performance of the web interface. This file is automatically updated every hour. This means however that if one makes a change in the TLDD it will not be visible in the search interface immediately. In order to force the software to update the cached file, one can add the parameter alltarget=1 to the url.