It could be hard as autosplitters and load removers often read memory to detect and it depends if you reliably detect a change without it approaching modifying the game in any way. I suggest trying to get in touch with the creator of the original auto-splitter perhaps or someone who knows how they work. There might be a setting to remove 'X' amount of time from the final run to essentially automatically change the time to the correct stopping point.

If you use LiveSplit It should autodetect one when you select the game in the settings. I think this is the load remover file if you want it separately for LiveSplit. Not sure about elsewhere.