Carbon in filters and medication?

On average activated carbon works for about 2 weeks, depending on individual tank conditions. Since most home aquarists won't have the means to confirm whether the carbon's absorption capacity is indeed maxed out, 2 weeks is only an estimate. Some say that maxed out carbon can release its toxins back into the water, others disagree. Anyway it's always a good practice to change the carbon regularly.

I presume you have one of those filters whose filter pads are integrated with the carbon as a single unit? Those have a big disadvantage, as you've discovered in this scenario. I have a HOB filter for a small tank and I never used the filter pads that came with it. I use individual wads of filter wool and permanently have a small bag of sintered glass media inside. Carbon was used only on ad-hoc basis, never continuously long term.

If you remove the filter pad for a new one, you'll lose much of the existing beneficial bacteria. Well, you can chance leaving the pad in, but monitor your tank closely. I haven't used that particular medication before but many of them color the water intensely. If after some time your water clears up quite quickly, then maybe the carbon is still active.

Yes you need to remove the carbon. After 3 months there is a good chance that your carbon is significantly reduced, if not completely void of it's ability to absorb organics from your tanks water, but that is dependent on a lot of things: what kind of carbon you are using, your fish load, your feeding habits, whether you have live plants etc. So there is no way to be sure about it's ability to absorb the medication. The only sure thing is to remove it. I would suggest that if you don't have filter media that allows you to open them and remove the carbon that you sacrifice a set. Cut them open and dump out the carbon, then replace them with new ones once the treatment is complete. After that you can keep the old ones around and use them in the future when medicating the tank is necessary.

I want to say first, that I really really liked Still's input here and advice. I'm only answering in to offer you another possible solution that I feel will be at the least, just as effective, if not better. You can buy yourself a nice big Poly Pad at most of your LFS's and cut that into strips and add that in your tank. This should help assist with absorbtion of the medication, maybe not quite as well as carbon itself would, but the advantage you have with Poly Pad is you can re-use this.

The disadvantage would be that if you can't put the strips into your filter itself, it might not absorb as rapidly or effective as the carbon, but it will help you get rid of most stuff in your tank. You can tell how well your poly pad is progressing by observing the color change in the pad. When it becomes all brown or black, rinse it off with bleach, soak the bleach out of the pad, and you can re-use, or just buy new pads and cut out sections as needed. It certainly isn't expensive, and beneficial bacteria can grow on this as well.

Poly may well be a good option for you in this case with having the filter packs that have both mechanical and chemical filtration combined. Not only could you save some bacteria by just leaving a pad in place, instead of cleaning it off, but should you change out your cartridge, you'll have less nitrogen compound effects from doing so, by having several sections of pad in your tank. It will effectively allow you to suppliment your bacteria bed and help remove excess meds.