OK, not sure what copper medication you're using, or if Cupramine is different in this respect from other copper-based meds, but here is what Seachem has to say about the topic:
Q: Will the Cupramine kill nitrifying bacteria in the filter? I used it to treat the parasite problem in a 20g quarantine tank. Three days later, I tested the ammonia level, and it was about 0.5 ppm. The copper level was about 0.25 ppm, and the nitrite level was about 0ppm.
A: Cupramine may slightly retard the bacteria but overall it is safe to use and won't adversely affect the nitrifying bacteria. The reading of ammonia you're getting is most likely a false reading because Cupramine contains an organic amine which is very similar to ammonia in structure and the test kit is likely not able to distinguish between the two. You could try our MultiTest: Free and Total Ammonia test which does not have this issue and will not give a false positive... or you can use our Ammonia Alert which works on the same principal and will show only free ammonia.