The safest thing would be to download it and copy your save files and such over to the new folder so you have the old folder as a backup. Any saves from v1.3.1 should work fine in v1.3, and vice-versa, since the only difference is in how the game data is handled while the game runs.
If you by skipping mean holding down to double the cutscene speed, then that should only make the game skip every 2 frames, which should only affect performance in places where a lot of new data is being handled, and then that also depends on how strong your PC is I think.