FYI, the ammonia tests most reagent test, test for it TOTAL ammonia.
this is both NH3 and NH4 (ammonia and ammonium)
so yes unless your test is specifically for ammonia(NH3) you will get a reading of total ammonia including NH4.
prime breaks the chlorine /ammonia bond ...gets rid of the chlorine and bonds Hydrogen to the NH3 (ammonia) this creates NH4 (ammonium) which is less toxic than NH3.
the reading should go to ) shortly( a few hours) if the cycle is not affected and the bacteria are present to eliminate the ammonia..
if you are still getting a reading of .25 or higher after a few hours than you need to do water changes to compensate..the bacteria that consume ammonia will consume ammonium.