If you have or get epididymitis will your sperm die while you have the infection?

Not necessarily. One can have infection in the genital organs anywhere from the testicle, the epididymus, the tube, the seminal vesicles, the prostate, the urethra or elsewhere and still have live and potent sperm. Certainly in a localized area such as the epididymus, some sperm may die due to the surrounding infection. Interesting question!