Read the label on your dechlorinator. It ought to lock up ammonia. You might have to dose just a little more, it will say so on the label. Prime, for example says how much product will lock up how much ammonia.
From Seachem's web site, Prime page:
Use 1 capful (5 mL) for each 200 L (50 gallons*) of new water. This removes approximately 1 mg/L ammonia, 4 mg/L chloramine, or 5 mg/L chlorine.
Note that mg/l is the same as ppm. Fully read all the directions, do not JUST dose per the portion I quoted.
Some test kits will still show ammonia, even when it is locked up. You might have to get the ammonia test that is manufactured by the same company as your dechlor to get some idea if there is still some free ammonia or if it is all locked up.
Yes, it could have come from disturbing things.
It sure could have come from chloramines in the water, or ammonia in the water.
2 hours is not too long for the bacteria to be exposed to the air, as long as it was still humid deep inside the media. The bacteria live just fine in damp locations, they like the extra oxygen in the air.
You might have lost some bacteria on the outermost parts of the media, where it got the driest, and you might have lost some in the substrate, or by removing some plants. The bacteria live on the surfaces of the leaves, and on the upper layer of substrate where it is closest to the water in the tank for oxygen and fresh supplies of ammonia.
If it goes on for more than a couple of days or you are worried about it you can go buy some more bacteria. Look for Nitrospira species of bacteria. These are the actual species that are part of the nitrogen cycle. Do not waste money on anything else.
Look up both the test kit and the dechlor you use and see what the story is.