Firstly, I'm not a dev of any game based on SugarCube engine.
Secondly, I've done some debugging based on parts, which you carved out (good job for finding that).
Apparently, new scripts which are handling event of clicking are checking, if property State.variables.presentContentOnClick is either true or false, but at the same time does nothing and does not throw explicit error for any other value.
At the same time, my working hypothesis is, that when generating save whole property State is dumped into a file and because previous version of the game had no property State.variables.presentContentOnClick at all, event is simply started and exited without action or error.
Thirdly, for new game, property State.variables.presentContentOnClick is set by default to true.
For old saves, instead of going with explicit modification of index.html, at least for my tests, it is sufficient to start default index.html, load old save, then start Developer tools and add presentContentOnClick property using command
SugarCube.State.variables.presentContentOnClick=true
