Could chlamydia be undetected in my girlfriend's mouth for almost 5 years?

Extremely unlikely: First, chlamydia infrequently infects the mouth or throat. Second, chlamydia is rarely if ever carried as long as 5 years. Almost all genital chlamydial infections clear up within a year, even without treatment. Have you had a lab test to diagnose chlamydia? Or only symptoms? Nongonococcal urethritis (NGU) can result from oral sex, but not caused by chlamydia.