It was actually a bad flex-plate then, huh?
I've done many transmissions & I've never seen or heard of a flex-plate going bad. (I had a flex-plate on my old '77 Diplomat lose a few teeth, so I carried a wrench around to manually rotate it to a good spot to start it once in awhile too! But that was a starter issue that ate the teeth off by not fully engaging the starter / flex-plate ring gear.) In my mind a flex-plate is just a part that doesn't go bad... Guess I'll file this one away for future reference!
With that being said. I have never given much thought about, nor would I have ever had reason before to remove the flex-plate when doing trans work. It's also not standard proceedure to leave the torque converter bolted to the flex-plate when removing the trans. It usually wouldn't be feasable due to the increased distance the trans would have to be moved backwards in order to disengage the trans input shaft from the torque converter...