Is TS2016 deleting any mods?

It appears that TS2016 resets any mods I have installed.
I have a batch file that deletes any Blueprint.pak files and then installs any mods I have. However every time I leave the game and then come back later all the mod files are gone and the .pak files are back. Are we going to have to reinstall all the mods everytime before we start the game?
TIA
I have a batch file that deletes any Blueprint.pak files and then installs any mods I have. However every time I leave the game and then come back later all the mod files are gone and the .pak files are back. Are we going to have to reinstall all the mods everytime before we start the game?


TIA