Wait, there's something easier for the 3DS with A9LH:
https://3ds.guide/a9lh-to-b9s
You don't need SysNAND to boot for this to work, so you don't have to resort to NTRBoothax. Just update to B9S using this and then CTRTransfer through GodMode9.
As for the one without A9LH, that one should be done through NTRBoot. That's the expected behaviour with the magnet. It stays in sleep mode, so it allows you to use NTRBoot.
https://3ds.guide/a9lh-to-b9s
You don't need SysNAND to boot for this to work, so you don't have to resort to NTRBoothax. Just update to B9S using this and then CTRTransfer through GodMode9.
As for the one without A9LH, that one should be done through NTRBoot. That's the expected behaviour with the magnet. It stays in sleep mode, so it allows you to use NTRBoot.