I realized I didn't want there to be choices in the game and had to take them all out
Which i think one of best decisions that were made. Overwhelming majority of visual novel authors got stuck with updating their visual novels exactly because tried to make choices and different paths which lead to more and more effort required to update all paths.
Some partially solved this issue by making essentially only one path for player to follow, just with certain differences depending on previous choices.
Wish you all good luck in solving this mess!