I think you need to dig deeper to find the root of the problem than just a flexion test, because there is something going on if the horse is bobbing.
And I don't think a horse should ever go lame from being worked every day, after resting for 2 years. Sore? Absolutely. Lame? Hmmm, shouldn't. Either that, or you are working this horse too hard too soon for his fitness level, if he is coming up lame because of it. You wouldn't go run a marathon after sitting on the couch for 2 weeks, would you? No. You'd hurt something. We can't expect our horses to go full kilter either, if they aren't in the proper shape for it.