Did the expert staff at Flynn's forget to put any oil into the engine, run it, damage it, then put in gear oil or something else heavy to quiet the engine?
If it was gear oil, the owner who claims to know a lot about engines would have smelled the distinctive gear oil odor and commented on it, eh?
No idea why the filter was empty unless something in Flynn's actions caused the oil pump to fail. And, why did the owner get the flush, and why did he do the work en route? Was this flush just adding a flush solvent and idle the engine for the usual 15 minutes, or was it more?