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The mini-cycle might have been due to medication. Whatever the packaging says about not harming filtration. There are multiple bacteria/archaea species co-existing and interacting in the filter. Even if medication is not directly harming most well known types of ammonia oxidizing species, it may harm other microbes, which may contribute to the filtration indirectly.
For what I can figure there is a creeping bacterial infection in the tank. It is hard to get rid of those if you have scaleless fish, as medication does more harm than good to them. You need a very good clean, ultimately change of substrate (play sand will harbor pockets of rotting matter) and more flow. Consider UV Sterilizer, if it suits your budget, but remember they are not a panacea. UV will only help to remove bacteria from the water column, but it will not clean substrate. It will not fix fungal infections too, although fungus is usually opportunistic and will subside when your fish get better after cleaning and water quality improvement.
 
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