Your save files and other persistent data like CG unlocks are stored in a separate place on your computer than the game itself. You can just delete the old folder containing the earlier version of the game and then launch the new version that you download.
That said, I will recommend starting a new game for at least the next few updates, then use the Skip option at the bottom of the screen to fast forward to where you left off. There will be code changes in the game that could cause errors, in particular with displaying some images. I try to avoid needing to do this as much as I can, but since this is a developing game, I sometimes need to change things on the backend to make everything work for future content.
As long as you don't delete the separate folder with your saves & persistent data, you should be able to zoom through fairly quickly. It'll stop fast-forwarding when you need to make a choice or if you hit changed dialogue, like if I fixed a typo. I'm also adding additional scenes that you may see along the way. Otherwise, it'll take just a minute or two to catch up.