Other tips:
I use a Dremel with a cut-off wheel to trim fender stays while they're still installed on the bike. I've tried the official "mark, remove, cut, reinstall" method and have always messed it up.
It's tricky doing it while they're still installed because you can heat the metal enough to melt the plastic. I hold the end of the stay with a pair of needle-nose pliers, then use a firm hand and assertive manner with the Dremel to cut through before the stay heats.
Try using bolt cutters next time. Quicker and eliminates the heat issue.