1. tony is correct updating your sysnand will help
the problem is with the major inconsistencys between 6.0 and 10.3
i have a 2ds on 9.0 with emunand 10.3 and never get/had said problem except before i updated it from 6.0.0.12U
2. you can use that game to update but it is not advised as gamecard updates often contain stub files . . . stubs just make things harder and more complex or even impossible
3. god damn i am confused here dude menuhax works fine (btw menuhax was written for 9.0 or higher you know themes and all . . . if you are on 2ds 6.0 then it would not work . . . and if you previously were on 9.0/9.2 then . . . you have hard modded your 2ds for no real reason)
with the 9-28 rxtools build from this link
RxTools Nightlies by @WhoAmI? and menuhax i have a birth controol bootrate . . . 99.99% accurate . . . lol