All antibiotics have side effects and toxicities. Scaleless fish esp. suffer. You always have to compare harm/benefit. Usually its best to treat disease. Some antibiotics can harm your biology and set your cycle back. You won't know about this one until you try. I would keep dosing with stability periodically (once a week or as directed) until you know your tank is cycled. Worst case, the antibiotic will kill the bugs in the stability and your filter and you will need to repeat the process after the treatment is over.
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So I should cut the net open dump out the carbon in the net then place the net back into the filter?
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If the carbon is in a filter floss pad or envelope, put the floss back in. If the carbon is just in a bag, you can set the whole bag aside. Hopefully, there is other media in your filter.