how long can chla/gon be dormant in your system without symptoms ?
Your age is right at a statistical break-point for common causes of epididymitis. Below age 35, chlamydia and gonorrhea are the most common causes. Over 35, most cases are due to nonsexually transmitted urinary tract infections, with E. coli the most common cause. Your doctor probably ordered urine tests for UTI bacteria in addition to gonorrhea and chlamydia tests. In any case, you could not possibly have acquired gonorrhea or chlamydia through a condom, so you can expect those tests to be negative. (If positive, you can assume you were infected sometime before the recent sexual contact.)
The wrinkle in your case is the bike riding -- conceivably you could have traumatized your prostate gland in a way that causes testicular pain, mimicking epididymitis; or might have traumatized the testicle itself. So you should discuss with your doctor how certain s/he is about the diagnosis of epididymitis. There is no way I can judge that.
I hope this helps. Best wishes-- HHH, MD