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If the OS was reading/writing to the drive in real 4096-byte sectors instead of 512-byte sectors, then very likely the metadata of the filesystem, such as the MFT if you formatted this NTFS under Windows, is also expecting that. There's no way to fix that without completely translating/rewriting the MFT. That's all over the disk. You would need a utility that is specifically designed for this purpose; I don't know of any. Perhaps there is one and someone will respond with it, but I'm betting you're going to have to do what's in this answer.
– LawrenceC
Commented Oct 28, 2020 at 15:37
@LawrenceC You might be right about that, in which case going in that direction (updating the MBR/MFT/etc. to use 512-byte sectors) may turn out to be practically impossible. But what about going the other way, so we update the disk to be marked as having 4096-byte sectors? If this were possible then everything should be consistent, no? This seems to be what TestDisk does in software, but is there a way to make this permanent so that the OS, and therefore all other software on the machine, can read the disk properly?
– HappyDog
Commented Nov 8, 2020 at 16:15

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