The tank is not cycled if he removed the filter, and therefore having a bacterial bloom he is restarting the ammonia-nitrate cycle (op stated there was .25 ammonia present). There is not enough BB in the tank alone to keep up with the Ammonia and waste levels in most aquariums which is why we get filters to assist. When you removed the filters you removed an substantial amount of beneficial bacteria, enough to cause a bloom in your tank, which can kill off existing beneficial bacteria due to low oxygen etc.
Here is something for you to read to help you understand bacteria blooms. http://www.fishforums.net/index.php?/topic/246850-bacterial-blooms-explained/ the link is more directed toward having too much waste in the aquarium, but that can be caused by the bacteria needed to break it down has been removed and there is an increase of waste.
Here is something for you to read to help you understand bacteria blooms. http://www.fishforums.net/index.php?/topic/246850-bacterial-blooms-explained/ the link is more directed toward having too much waste in the aquarium, but that can be caused by the bacteria needed to break it down has been removed and there is an increase of waste.