if it's metal, it can be reworked. you should see the amount of work greg davis did to fit his 39.5s.
are you talking about for your girlfriends DII? i don't see any issues at all. just remember welding thin steel is far harder than the thick stuff.
EDIT: if it really worries you, you can weld in a brace out of some 1" flat stock or similar to keep it in the correct place (for panel alignment of fenders, hood, etc.) so that when you cut it out, it won't deflect or move.