So I got a new 3ds xl a while ago, decided to upgrade that mother with a 32gb sd card. I botched the system transfer somewhat. I forget how; Anyway nearly everything works fine (had to redownload a bunch of eshop titles, don't know about my game saves) except for the 3ds home themes.
Prior to the transfer, I always used the link between worlds theme. I love it. I turn the system off, turn it back on, theme would restart with it.
After the failed transfer, when i boot my 3ds up, it ALWAYS restarts with the default nintendo home theme of white boringness.
I have a feeling I might be missing an important file somewhere, but whatever.
I don't know if this is the same thing, but that happened to my regular 32gb SDHC card when I was having troubles with my XL. Eventually I was also getting "SD card removed" errors and the console even shut itself off at one point. Switched SD cards and hadn't had a problem since.
If the latter two things aren't happening to you, I suggest deleting and redownloading the themes as something was probably missed in the transfer as you said.
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Topic: New 3DS XL Themes resetting after restart
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