While I've never heard of engine braking cracking a flex plate, I'll go out on a limb and say that I think that it's possible.
That spinning converter is heavy and is applying a jolting force to the flex plate when the shifter is dragged down into a lower gear. A few times may not hurt anything but doing this on a regular basis might cause a tiny fracture which could snowball and become noticeable.
Back in the 50s, there were several catastrophic crashes of the new British Comet airliners over open ocean. It was determined from recovered wreckage that these planes came completely apart in mid-air due to a fracture so small that it required an electron microscope to even detect them.
If an airliner can break up from something so tiny then why not a flex plate too.
If the transmission has never been out of the truck before then my guess (and that's what it is at this point) would be that chronic slamming of the converter mass against the flex plate bolts could be behind this.
Careful examination of the old flex plate bolt holes may reveal something. If the bolt holes are slightly shiny or wallowed a bit that could point to downshifting being the cause.