How long ago was her injury? Is her sphincter relaxed and open (you can see a little poop most of the time) or is it closed tight like in normal dogs?
When she eliminates, are her stools normal or are they dry at the beginning of a bowel movement?
There is a common medication called cisapride (Propulsid). Does that name sound like the medication you had?
Have you tried adjusting the fiber in her diet and possibly a stool softener like lactulose syrup or Miralax?
If her bottom is healed, you won't hurt her. There are videos showing how to help a dog eliminate, but it sounds like you are already doing it?