I believe your issue is bigger than just a recently clogged filter.
My biggest piece of advice is to increase the frequency and % of your water changes. You have 1) a lot of fish 2) in a small tank 3) with large substrate which traps waste and uneaten food particles 4) with small infrequent water changes and you are starting to see the end result of this imbalance. You may need to age and heat your water in advance if the ph swings at all. Sometimes the ph of tap water can change after it sits for a day. I determine if this is the case fill a bucket with tap water and test the ph immediately. Then aerate it with an air stone for a day or if u don't have an airstone just let it sit for a day and test the ph again. Let us know what the results of both tests are and we can advise.
The next best thing you could do for the fish is remove the large gravel and either switch to a totally bare bottom system (this would be my first recommendation) or if you dislike BB replace it with a very thin layer of sand. If you do this you must make sure you don't crash the cycle in your tank, as a lot of beneficial bacteria have probably established them in your substrate. Additionally, toxic gasses can build up in substrate so I'd recommend to remove all fish to a holding tank while you remove the gravel, then do a 100% wc, then replace the fish. After this you will likely need to do huge daily water changes while monitoring the parameters of the water while your beneficial bacteria grow back to their optimal numbers on other surfaces in the filter itself.
What kind of filtration do you have on the tank?
I am certain this isn't the response you wanted to hear, and my suggestions will be first viewed with skepticism, but I can't see you having long term success with these fish if you continue the current regular maintenance routine. I'd expect them to slowly die off as their immune systems become weakened over time. I have been in your shoes and lost a lot of fish until I changed my set up and routine.