Well aware of Chisel update causing issues, and am aware that its probably what has caused this. I have tried using a copy of the instance pre chisel update and deleting the references to chisel blocks in the quests.Did you use an Auto Chisel in any of your quests? Updating Chisel changed a few item id names. If you load an old world to have Forge tell you what blocks have been removed from the world, those item will have to be removed from your quests before you updated the mods. Once they are removed you can update the mods and you'll be able to re-add those items to the quests, then you can save again.
I have however just been informed by the players on my test server for the pack that there is another reference to limestone that I'd forgotten about, so I'll give it another shot