by Bret Miller.
As long as you copy all three components of Moodle to a new location (php files, database, moodledata) and use the migration instructions (http://docs.moodle.org/25/en/Moodle_migration), there should not be any issues with future stability or performance simply because you copied your installation. And as long as use use the official methods of removing content (like resetting a course), that also should not affect stability or performance.