Hello @xim,
When it was just released they were some issue yes, the "cooking" process could mess up some files when the user for example installed RWE 2 in the TS (railworks) installation directory, which is a bad thing to do, RWE 2 should not be installed in the railworks directory but should be installed anywhere else on the computer like any other regular software/game.
Since the release a lot of work has been done to prevent issues and I have not received reports of any major breaking issue since a lot of time now (more than 1 year). The cooking system is not modifying/deleting any TS assets files it is just a file reading process. The only files that are modified are the engines scripts files (this is mandatory for RWE 2 to work correctly and some TS addons like the "cobraone raildriver and joystick interface" use the same exact method) but they are not modified all at once. When you launch a driving session with RWE 2, only the script files related to the engine you want to drive are modified and once your driving session is ended, scripts files that were modified by RWE 2 are restored in their original state each times.
If you want to be 200% safe I always recommend to make some regular backup of your Railworks install directory anyway if you can, this is a good practice before any TS major addon/assets installation not just for RWE 2
If you have some other questions, feel free to contact me by private message !
Also thank you for your comment @FoxDelta99 !