Should be alright, you're redownloading the entire game so you shouldn't have any inconsistencies in the game directory with uninitialized variables in leftover scripts and what not.
As long as the game is clean without the mod, you can run them. You would need to delete the modded version and run the clean version. Or if you have enough Hard Drive space you can have 1 modded and 1 clean.
Feel you brother, i was like that some time ago, tho this results are in a bad day, usually it's 800mbps download and 800 upload. I'm not flexing don't get me wrong
