It is not clear exactly what you are asking. Do you have an Open/Create file function which is prompting the user? Or is it the Error Handler? The file prompts can be eliminated by wiring a valid file path to the appropriate input of the VI or function. A few of the file VIs do not have this input, but usually if you open up their diagrams you will find that they use lower level file fucntions with that capability.
If you need to modify a vi.lib VI, save a copy of it to a new location first and then modify the copy. If you modify the vi.lib version, other VIs which use that as a subVI may not work correctly. And, the next upgrade of LV will overwrite your changes.
Lynn