It is fair to simply assume that the carbon has been taking up all the medication and none of the medication has been killing off the ich parasites. So, if you've been putting in medication for two days, take the carbon out immediately and restart your count at zero days.
The problem with slightly used carbon is that it will take up some portion of the medication so the dosing won't be right. Partial doses are really bad because it will effectively selectively breed the medication-tolerant strains of ich and then when you start using full doses the population of organisms is resistant and won't be killed by that same medication.
So, in short, remove the carbon immediately and restart your count of treatment days at zero.