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Yes, antibiotics, in general, will de-cycle your tank. There are some meds that claim to not do so, and this is a possibility. There are certain bacteria that have never responded to certain antibiotics. Still, it's not something I would count on. I always make sure i have extra filter media running in a separate tank.
Otherwise, you can refrigerate the filter media in a ziplock bag with some tank water and keep it going during the length of the medication. Run fresh AC in your tank when you're done, then replace the old filter media.
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