I'm not sure about a script step, but you can convert all your files at once by opening FileMaker 12, selecting File > Open, and Control or Command clicking the files you need to convert. You can then specify a location for the converted files to be saved to.
Is there a script which will convert 40+ FM11 files to FM12, or do you have to do it one by one?
Doing them all at once is the best way. You can drag and drop the files onto the application icon.