If your urethral discomfort continues, the recommended approach would be 1) to determine whether actual urethritis can be documented (abnormal discharge, increased white blood cells in the urethra) and, if documented, to treat
plus metronidazole (Flagyl is the most common trade name).
In any case, don't worry about long-term or serious health effects. None are known from persistent or recurrent non-chlamydial urethritis. It is an issue of comfort only.