Wanting to remove the built-in levels from the levels list is a perfectly valid reason to mess with that zip, it's what I did for V6HS (you know, that video which I was supposed to put on VHS and then back to a digital format and then to upload it)
The world isn't going to explode if you screw data.zip up, if you notice that VVVVVV crashes after doing something with the zip, then you know you did something* wrong and all you need to do is place back the original one to get it back working.
* that "something" can be using Windows explorer to modify the zip