But games like Animal crossing and Pokemon x/y don't have save data back up and my friend did a system transfer from the pokemon x 3ds which had the game pre installed and her save data was gone completely after the transfer.
How did that loss of data exactly happened? Did they left the source SD Card still in even after the System Transfer finished and reaches the HOME Menu? If that was the case, then they could've pulled the source SD Card out as soon as the source system says the transfer is complete and put it on the target 3DS system.
The games that normally won't let you backup your save data actually allows you to do so if you choose to delete the software and preserve the save data. Very few games actually won't let you do backup whatsoever, but so far the only ones that falls under that category are the GBA VC games exclusive to 3DS Ambassadors.
Even if you didn't manage to backup those datas, the System Transfer should carry everything over just fine.
Since you're transferring to a New 3DS model rather than either 2DS, 3DS or 3DS XL, it's not a bad idea to choose the "Wireless Transfer" method, but it can get pretty long. This is the simplest out of the three methods. How long does it takes depend on how many GBs of data you have on the source SD Card, but it does take at least 4 hours to complete the transfer. Be sure your Internet connection is consistent enough, or you might lose your data if the Internet disconnects.
A faster alternative to the previous method is to pick "Low-capacity Transfer". It'll transfer the same exact content. While the downloaded games will be gone, the saved datas will be preserved. All you need to do is to redownload them and you should be fine. I highly recommend this method if you don't have an appropriate screwdriver to get the New 3DS's back plate out. Takes overall 30 to 45 minutes to complete that system transfer, and longer depending on how many games you have to redownload afterwards.
The best method of transferring is to copy everything from your old 3DS's SD Card to your computer, and then copy all of these datas to your New 3DS's microSD card. You'll need a #00 Phillips-head screwdriver to be able to remove the screws holding the back plate in place. The entire transfer process lasts no longer than anywhere between 30 and 45 minutes.
Still want more information about System Transfer?
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