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I'm writing a Bootsector for Advanced Format Drives (4KB per sector hard drives). On 512-bytes-per-sector drives, I know the boot signature is at offset 0x1FE. On the Advanced Format Drives, will the boot signature still be at offset 0x1FE or will it now be at offset 0xFFE?

I am totally guessing....
If you run IBM PC BIOS (legacy BIOS) then the drive reports that it has 512 byte sectors, it emulates the old standard of 512 bytes per sector.
If it is UEFI, then the boot signature is irrelevant.