As part of the reconstruction of the system, we had to take it apart first.
First I pumped out almost all of the water in the shorter IBC container that had served as the sump tank.
Then i caught the 10 or so tiny Bluegill fish that were in the tank.
Next was the larger Tilapia tank. The water was too murky to see any movement in there, but I stood vigilant with a net and bucket.
As the water receded, I noticed the discrepancy in temperature between the 200 watt aquarium heater hanging by its cord ( set to 75 degrees Fahrenheit ) and the floating aquarium thermometer, which read, 62 degrees Fahrenheit.
I do not think warm-water Tilapia can survive such low temperatures.
When the tank was almost empty, a ridge of mud became visible at the bottom, which smelled very bad. There was still no sign of the Tilapia, not even part of a skeleton.
Incidentally, I do not recommend emptying a IBC container fish tank by turning the handle of the ball valve at the bottom. The valve could have some unseen crud stuck against the ball, and it may not be possible to shut it tight again. If there are live fish in there, this could be a big problem. Better to pump out the tank and leave the ball valve alone!
I ended up shoveling out the last of the water and mud, a very nasty job.
We will never know for sure what happened to the Tilapia, but this is my theory: they died of cold some time ago and completely dissolved in the water. Somehow the Bluegill in the sump tank survived the elevated ammonia levels this must have caused.
Part of the problem was that colder water from the grow beds kept flowing in and overwhelming the ability of the heater to keep the water at 75 degrees, meanwhile, heat was not prevented from escaping through the thin walls of the tank.
To hopefully prevent this from happening again, we will insulate the fish tank next time.