I personally downloaded the Steam version and just moved the save folder from my Itch.io copy into the Steam version, that way your game will auto update and keep all user data.
Though, if you want to keep using Itch.io you can just go in to the files and drag the save folder from the old copy of the game (the main folder) to the new copy and replace the new save folder and you'll be able to continue from where you left off your save!
Hope this helps ^^