Good catch Meyer but I do not believe there would have been much of that bacteria in the water anyway. These bacteria generally live on surfaces rather than float around. Now if the lava rock had been used in a pond filter then maybe... However I would like to post the following article for review, which suggests that the bacteria do not just up and die due to a lack of food.
http://www.practicalfishkeeping.co.uk/content.php?sid=4780
Here is another link that shows they do not die but rather go dormant until conditions improve. Although he is trying to sell product and doesnt post a source, he does say his research is peer reviewed etc... just dont see the proof...
http://www.drtimsaquatics.com/nitrifying-bacteria-arent-human
This is true...providing there is another 'food' source. Actually, the use of the word 'food' is wrong. As with all life forms, Carbon is basic building block in nutrition. In the case of nitrifying bacteria, the oxidation of Ammonia or Nitrite, as the individual case may be, is only a side catalytic process to the main goal of consuming Carbon.
Anyway, what is stated in these two (2) papers only holds true in the presence of water. This was not the case in JB's plight. With the exception of the pond and source water that he added, every surface of the stock tanks, plumbing, filter and lava rock media were dry and had been for at least a year. The source of nitrifying bacteria in this case, as it is in new ponds, was the water itself. Granted, nitrifying bacteria are more comfortable snugly tucked away in its biofilm home, but because regeneration is an ongoing process within biofilm, sloughing is also an ongoing process. Some of it may partially retain its identity as Floc. The rest of the bacteria become planktonic if only for a brief period of time before it re-attaches and recolonizes a different location. AOB can most certainly achieve motility when required. The first quoted paper states this fact.