Yes, it renders the treatment much less effective. One of the drawback of copper is you cannot use any resin/media/additives that would allieviate nitrogens as they will also affect the copper itself.
If you still want to use the chelated copper that's fine, you just need to start from square one. Do the water changes and carbon use suggested by macman7010 above. Test to be sure no copper registeres and then dose according to the instructions. Be sure you have the appropriate test kit for chelated forms of copper and test at least twice daily to ensure the concentration is being properly maintained.
As for the ammonia, the only way to deal with that is via water changes. The easiest way is to have your change water in a pail you are willing to part with later. Dose the copper in the pail to the appropriate concentration (5ml/4gal water volume), that way you do not have to guess what's been removed and what to add that will bring it back in line.
Remember, no carbon use, resins or anything else that will sorb copper. Inluding sand, rock or any other CaCO3