I’m not sure what code you cut and pasted, but you may very well have your 2012 project reusing files from the 2011 project. To see where the files are coming from, click on the Files tab on the project, and it will show where the files are store.
The library files such as WPILib are certainly changeable by you, but it isn’t common that you accidentally change them, especially from the operation you describe. More likely, you made changes to the Team Code to refer to a new location for a function or global for example.
At the time of the save, there is a link in the Save dialog for details. They are somewhat generic, but will tell you what the modification is. This is usually enough to make you comfortable clicking save or Don’t Save.
After the file is saved, a diff with an official file is the only way I can say for sure. Unless you opened up vi.lib files and made your own edits, it is very unlikely that you caused an issues. I’ll go with Joe’s explanation.
I would encourage you to look at the Files tab and determine where your source is coming from though. The LV project has a way of trying to help you by adding links to files that are in locations you didn’t realize. Then later, you’ll clean up your hard drive and boom goes the dynamite – your project is broken.