It is objectively and factually accurate that this is an optional puzzle with a non-essential reward. I said that in reply to someone who mentioned not wanting to start over. The 'and so what' was that there was no need to start over.
There are mutually exclusive choices and multiple solutions to some quests, so there is no way to enjoy all the game content in a single playthrough.
The problem with games started in the unpatched version is not a case of being unable to fix, but being very limited in scope and any fix having the risk of causing serious issues for everyone.
For reports of this happening with a game started after either patch was installed, thus far nobody has contacted support about this, so the programmers have nothing to go on to be able to confirm or reproduce the problem, let alone fix it.