Untreated conjuntivitis in a cat?

Conjunctivitis in cats can cause scarring, but the bigger issue is that sometimes the agent of the conjunctivitis becomes permanent. Most eye issues in cats are caused by viruses. So while the majority of the issue may resolve (the concurrent bacterial infection), you may have some permanent eye watering, and she may be contagious to other cats (if you have others). If it does turn out that her eyes are watering, you might consider adding the supplement l-lysine to her diet. L-lysine replaces l-arginine in the body, and l-arginine is necessary for viral replication. So it can help minimize the impact of viruses. Good luck!