Not that I'm aware of using a homebrew app.
Depending on the region, the HOME Menu extdata is saved on the SD card in:
- Nintendo 3DS/<ID0>/<ID1>/extdata/00000000/000000XX/00000000/00000003
- JPN = 82, EUR = 98, USA = 8f
For HOME Menu saved theme layouts, all three regions share:
- Nintendo 3DS/<ID0>/<ID1>/extdata/00000000/0000165c/00000000/00000003
You can't simply cut and paste these files over from one SD card onto another between two different 3DS systems due to encryption.
It might be possible to decrypt these files with GodMode9 and swap them if you navigate in the
[A:] SYSNAND SD drive.
Edit - Forget the above idea. I just tried it between my niece's n3DS and my n3DSXL. Her layouts from her SD card didn't transplant onto my card when navigated in [A:] drive. Also, there are
CMAC corrections for those two files.
How I came to determine either or both
00000003 files control layouts was through a hash comparison between a set of
Nintendo 3DS folders. The only change from one of them was saving an additional HOME Menu layouts.