If epiddymitis has cleared away after 3 months without any treatment, could it have still left some damage despite a normal ultrasound?

Yes, afraid so: Sperm are about the size of a red blood cell , 5-7 microns. US IS good but cannot detect damage in a tube system that transports sperm cells . It is likely the epididymis will be ok. In Urology we say epididymitis once, 50 to60 % chance of 2nd attack. Have it twice, about 100% chance of 3rd time. Wear a supporter when working and never do heavy weights with a full bladder. Get to doc fast.