Clownfish staying on the bottom for months but is healthy kinda... HELP

[That1guy07]

So I have had an ocellaris clownfish (1 1/2") for about 4 months now. He has been in my 45 gallon reef with my true perculla clownfish (Black onyx Picasso) female (2 1/4"). When I first introduced him, they had a bit of bickering but then quickly paired up. They were paired for about the first 3 months. They slept together, wouldn't leave each other, and defend their area near my heater. But sometime outta no where my female clownfish started attacking my male clownfish. This happened for a while until my male clownfish was laying down on the other side of the tank. She literally grabbed one of his pectoral fins and threw him out of the water. He almost landed out of the tank. Anyway, he had torn fins and laid down on the other side of the tank from my female. I saw he was in rough shape and didn't want one of my emerald crabs getting a hold of him during the night. So I put him in a surface floating breeder box made for guppy's that I had from my freshwater tank years back. He was there for 3 weeks while his fins healed and slowly got him back to health. He always stayed on the bottom of the box. About a month ago, I let him go back into the tank, his fins were healed, color was back, and was eating well. The female clownfish didn't even seem bothered that he was back. She would casually stroll near him and say "hi". The problem was he was still on the bottom of the tank. just laying there. He was breathing normally. Another thing he did was he didn't come up to eat anymore. Instead he would wait for the food to come to the bottom of the tank and kinda sift through the sand with his face until he got some food in his mouth. Every night when the lights go out, I sometimes turn on my flashlight and see him swimming back and forth in the tank really fast. He doesn't stay on the bottom when he does this, he goes to all levels of the tank. Since I released him back into the tank, I have done water tests everyday. Ammonia 0, nitrites 0, nitrates <0.5ppm. He is healthy and breathing normal, he just doesn't wanna swim during the day and it has me really worried. Can someone please give me an explanation on this to help me out? Thanks. Heres a picture of him taken just now. #reefsquad

 

[Peace River]

It sounds like a learned behavior based on his previous trauma and the dominance by the female. You could leave everything the way it is and see if he gets more bold over time which is possible but IMO not likely. Another option would be to rehome him and decide whether or not you want to introduce another potential mate. Good luck with whatever you decide!