If you migrate to SD2 using Storage, it’ll make a copy of the BIOS folder on SD1. The system will automatically use the BIOS folder on SD2 if the directory exists there.
If you want the system to use SD1 instead of SD2, you would need to manually remove the BIOS folder on SD2 yourself.
You can also sync the SD2 folder back to SD1, which just ensures that whatever changes you might do to the folder gets cloned to SD1. The SD2 folder will still be there in this case.