Installing the patch doesn't affect your save files, so you don't have to restart from the beginning.
I believe it may reshow the intro once, though.
You can also backup your saves at any time to be totally safe. Just hit up the c:\program files\aquaria\save directory and copy and paste everything into another directory. Just make sure you're copying and pasting and not just moving.
Anyways, I have to sleep for a bit, but if you run into more problems you can shoot me an email.