This method is where i found from GBA temp. Some users said actually the dstwo can updated with the 3dsxl even on a new firmware. That is amazing me. All we know that if your 3DS console is updated to the newest firmware, your flashcart cannot be updated with that 3DS, you have to use DS or DSi to update it. This is very inconvenient if you just have one console.
OK, let’s see how to do that: when you download the dstwo update patch , unzip the file, you will find a “dstwoupdate.dat” file, just rename it to “dstwoupdateb.dat”, then put it into the root of your sd card, insert sd card in your dstwo, and start dstwo on your 3DS. (don’t forget put the kernel in it also) You will find the screen show “error” with black screen as same as the card cannot work on the console. But don’t power off, just let it be, and wait. After more than 3 minutes (actually i waited 10 minutes), during this time, the screen is still black and show error, not any change, but don’t power off because it is updating actually, you cannot see the progress but it is doing that indeed.
When enough time passed, turn off your 3DS and delete the “dstwoupdateb.dat” file, then start it on your 3DS again. Your dstwo can work on 3DS newest version perfectly!