Prime® works by removing chlorine from the water and then binds with ammonia until it can be consumed by your biological filtration (chloramine minus chlorine = ammonia). The bond is not reversible and ammonia is still available for your bacteria to consume. Prime will not halt your cycling process.
I am going to assume that you were using a liquid based reagent test kit (Nessler based, silica). Any type of reducing agent or ammonia binder (dechlorinators, etc) will give you a false positive. You can avoid this by using our MultiTest™ Ammonia kit (not affected by reducing agents) or you can wait to test, Prime® dissipates from your system within 24 hours.