Search your computer for a folder called user.lib, it should be in the same directory as the Labview.exe. Usually the path is like the one below, but it depends on your installation options.
C:\program Files\National Instruments\Labview 6.1\user.lib
Open all the files you modified, and change the inputs back to the way they were before you changed them.
On the front panel of each VI, right click on each input control you changed, and select Data Operations, then click "Make current value Default". Save all the VI's.
Next, change the controls back to values that work for your DIO work, click the "Make current Value Default" on each control, then resave the VI in your User.lib location WITH A DIFFERENT FILENAME. Use the "Save As" command un
der the File menu. These are the files you want to save in your User.Lib folder.
Now when you want to call those files for your special DIO work, you use your custom files which are saved in the user.lib folder, not the files in the DIO menu.