I'm pretty sure that replacing it doesn't mean it will remove the entire files
Viewing post in Baldi's Basics Plus Mod Menu comments
DO NOT DELETE THE BALDI DATA FOLDER BECAUSE IT HAS THE FILES IN THERE instead copy the folder (if it has baldi data on it) and do not delete the folder go to ur game folder and go to ur current baldi data and streamingassets and create the folder called modded and put the folder in there. the folder im talking about is like alexbw145.baldiplus.pinedebug