i didn't pick up your phrasing but from what i understand you made an change in the code so you don't unlock something you shouldn't now so people aren't frustrated when they pick some late game recipe in the early game but because you put the Trueschist in the journal first it was searching for the old flag table that you removed and leading to the the events that needed that flag to don't find the flag in the table as the corresponding flag had stop processing?
Not quite. In previous versions when you found a hint in the library it would set a variable called like "marbleHint" to true. Then, in the Cave passage, there was a section checking to see if "marbleHint" was true and if it was, it would give you the option to search for some marbles.
Now when you find a hint it instead sets a part of an array to true instead. "hints[marble]" for example. The twine compiler didn't complain about it because the old variable technically still exists it's just no longer used.