There is a lot things that need to be answered before putting our green thumbs on how to get your tank back to a good stable tank.
You have a protein skimmer, great that will help.
You didn't mention what kind of biological media you have for filtration. That is your key to breaking down ammonia and nitrites to nitrates. Microsomona breaks down your ammonia to nitrites. Microspira and Microbacter break down nitrites to nitrates. This is your beneficial bacteria. Anaerobic bacteria is what breaks down nitrates to the gas form and bubble it up and out of your tank. This bacteria takes time to achieve. Also you may never achieve it with in your rock work or biological filtration. Your rock needs some deep porosity for this bacteria.
If you are using an API Nitrate test kit. Listen up to this. The laser etched line for 5ml maybe off. You could be putting in only 4ml of water. Thinking it is 5ml cause you filled it up to the line. So your test result will be off. Also if you do not shake that #2 bottle perfectly from day one like it is your job. The powder on the inside will stick to the wall and EVERY test result will be off after that. I had this happen before. Reading 80ppm when it was 2ppm. Which is ridiculously unacceptable. This may be your reason for reading 50ppm.
As for the biopellet reactor. Don't bother. They are hard to control for what you want to achieve. Plus if you were going to go as far getting all this. You are better off buying a bigger tank, a plate of Marine Pure to hold a ton more beneficial bacteria, and add more & better live rock to hold more beneficial bacteria to break down all the bioload.
Also make sure your chaeto is being lit all around. Also the middle. If the middle is not being lit up to get photosynthesis. The inner part could be dying causing a nutrients factor.
Plus I have no clue what chaetophilia is. Sounds like a phobia of chaeto morpha haha
