Does RW enhancer2 cooking change anything in the Railworks folder? Or does it leave all those files on their?
No TS asset/route file is modified/touched during the cooking process. The only files that are being modified is the scripts (but not during the cooking process) because this is required for RWE 2 to work correctly. When you select a scenario or quickdrive in RWE 2, the script of the engine being driven by player (and only this one, so only one file at a time) is modified and then after the RWE 2 play session the file is immediately restored in it's original state. With the new content cooking system everything has been carefully checked in this regard.