It will be fine if you delete the 14.1 folder containing the Game.exe file. By doing that, you'll have to use the Game.exe inside of the 14.6.2 folder instead to operate the game in correct version.
Overall, just make sure the Game.exe file you're using is from 14.6.2, not 14.1. Also, deleting the 14.1 folder will not affect your save as your save file is located in the Pokemon Reborn Section of the Saved Games Folder on your Computer.