Drupal: HOw to recreate a function within a module so it won't be over written on update

i had to make a change to one of the files in commerce_discount.  I added a join to the query so I could see another field in the product display.  I realized/remembered that should i need to update the commerce discount module, I will lose the changes I made.  I figure  I need to create/recreate the file with my changes, but how do I do this and call the new file and where do I store it so it will not be overwritten?

So for example, if I have made a change to coupon_discount.module, how do I recreate it?