Also, I am not worried about them living together at the moment, as they have been doing so for months, and if he was able to reproduce they would have done so by now. Except for Clara's eyes they are both quite healthy and eat very well.
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You should be worried, it is a big deal. You not knowing which of your snakes shed is one warning sign. You should keep track of each animal. If you cohab you can't tell which one shed, which one pooped and if they regurge you won't know which one did it. Just because your male is injured there is still a very good chance he is still able to breed and even if he is impotent he will still try to breed which will be extremely stressful for the female.
Cohabbing is dangerous and you are putting your animals health at risk. They may seem happy to you but they are not. The activity and cuddling you see is stress and that stress can eventually make them sick. I cohabbed two corns for 5 years and they were cohabbed before I rescued them and they never breed until the 5th year I had them. The female was to small to breed and it was dangerous and she was extremely skinny after laying 14 eggs. After she put weight on I put her back with the male where he continued to try and mate with her. He would also "cuddle" with her in the hide, and one day I saw him pushing her head against the wall of the hide. I don't know how many times something like that happened because normally I could not see inside their hide. If I kept them together they would have killed eachother or he would have mated with her till it killed her.
I didn't realize there were problems with cohabbing until there was a big problem, that is when I realized all the warning signs. I even argued with Beth about cohabbing, which I remember very well and feel bad about agruing with her because she was right and I am glad I finally listened to her. It is so much better not cohabbing and it feels better knowing there isn't even a chance of my snakes getting hurt or sick by cohabbing. We can only tell you what can happen and the experiences we've had but in the end it is your choice whether to risk it or not. We are just concerned for the health and well being of your snakes, which is why so many people stress not to cohab.
You should atleast go and buy a clear rubbermaid tub (or similar brand), put lots of holes in it and keep her in that until you figure out what if anything is wrong with her eyes. This way if it is something contagious it doesn't spread to the other snake.