OK I re read the post, you should of put your media from the filter in a bucket of tank water, or left it running (if it doesn't loose its siphon) and even adding or removing things from the tank like gravel that had Bb in it you have to add liquid bacteria back into the tank unless you have a lot of media BB is grown on
How much water did you take out you should never have to go over 30% weekly learned this the other day as well, 50% can be to much.
Reason why you should of put media in a bucket of tank water is because it's going to be the same temp the tank was running at, temperature change/shock will kill beneficial bacteria that's on your media (aquarium adventure) told me this
I would get some liquid bacteria and dose the tank and do only water changes don't touch the gravel until you start getting your parameters back in order.
Never ever ever rinse media off in anything but tank water not even treated water, the only thing you clean with regular water is the plastic casing, and you don't thoroughly clean the media just dip it in the siphoned water from the tank, swish lightly to get big debris off and put it back in.