Is he asking about the rider's backrest or the passenger's?
If it's the passenger's, I would be concerned with drilling new holes in the fender only because they wont have the support of the fender struts.
I assumed he was talking about the sissybar backrest. And if the mounting bracket holes are the issue, holes can be drilled into the sissybar bracket to match the fender struts. Good point, Dan.
In addition to the support issue, once you drill holes in anything they're there forever. Best to modify the cheaper of the two components: that being the mounting bracket for the sissybar.