I wouldn’t worry about it with an Indie game. We have used the feedback that we get to change Lemons Must Die. Basically we have been open to critism, but tried to channel it into specific things that we could alter. As a result the controls and camera perspective are very different than when we started and it was effected some of the in game matinee’s and tutorials to help orientate the player better to what’s going on. For the positive feedback area’s we’ve made sure not to mess with those parts that are working well.
When you talk about messing stuff up, you sound like you don’t have a back up. You really need to use version control for anything other than a throw away project that you don’t care about losing. Unfuddle, Assembla, Amazon, GitHub are just a few of the many websites where you can host your project. That way if you screw up, just discard your changes.