If the payload was stored in the save, it would still work. I never reinstalled Ironhax or anything, just came on one day and couldn't access it.
No, it would not. You can't change your payload because you need homebrew access to change what's in your save file.
The error you get is because your payload is the wrong one for your firmware. Changing the boot.3dsx won't do anything; it doesn't get to the point where it would try loading the boot.3dsx
You are on 10.3 and your save has a 2.1 payload in it. Meaning you have a payload for 10.1 or lower. Wrong payload for your firmware, and the only way to change it is to have access to homebrew launcher via another mean.
You just came on one day and i wouldn't work, meaning you just had it on 2.1 for whatever firmware you were on at the time, then decided to update your 3DS thinking your ironhax would work without updating the payloads.