1. make a copy of your rom and add 512[1] bytes in the begining of the file (use some snes rom editing software, dd[2] or ipsbehead[3] if you will)
2. patch the modified rom
3. strip the first 512 bytes from the patched rom
4. generate a patch from the roms
5. delete the modified rom
6. enjoy using your unmodified rom with a working patch
7. get a gf


1:
512 bytes is the header size iirc

2:
dd if=/dev/zero of=headed.sfc bs=512 count=1
dd if=original.sfc of=headed.sfc obs=512 seek=1
*apply patch to headed.sfc*
dd if=headed.sfc of=headerless.sfc bs=512 skip=1
*create patch to change original.sfc into headerless.sfc*
*remove headerless.sfc*
*play original.sfc with your new .ips/bps/whatever patch*


3:
https://github.com/heuripedes/ipsbehead
(if you want to compile it to use in windows, just run gcc ipsbehead.c -o ipsbehead.exe)