If I were you, I would check the Nintendo 3DS folder to see how many (random characters) folders you have present. Each one corresponds to a different NAND (either EMU or old formats). You should only have two of them, one for each NAND. If you have more than two, then yes it would seem like the one originally encypted for your console is invalid now.
Also, there is way more to running Gateway on 11.2 then just creating an emunand and running Gateway mode. Gateway can ONLY be used through BootCTR9, since it uses binary payloads, not firms. You need to go to this thread and follow the directions to get your Gateway to boot correctly.
https://gbatemp.net/threads/tutorial-using-luma3ds-gateway-on-b9s.431691/
Three pages and not one person thought to tell you....... Le sigh.