The SMD and BIN formats are two different formats:BIN
SEGA GENESIS (C)SEGA 1992.SEPSMD
SONIC THE HEDGEHOG 2
EAGNSS CSG 92SPOI H EGHG2
OI H EGHG2
The SMD format is interleaved/swapped, and might have a 512 byte header at the beginning. The emulator you're using probably doesn't notice the .md or .bin, it will determine which format the ROM is in and play it correctly. Some or most of your games that have a .md extension are actually in BIN format.
What I would do is convert the ROM to BIN format, apply the patch, then convert to SMD format. For this you can use uCON64
(it's command line utility).
Convert to BIN
ucon64 --bin game.md
Convert to SMD
ucon64 --smd game.bin
uCON64 will show you which format the ROM is in. Look for this in the output:BIN
Backup unit/emulator header: No
Super Com Pro/Super Magic Drive/SMD
Backup unit/emulator header: Yes, 512 Bytes