First, the background:
I have two 3DS systems with 2GB SD cards, and one 3DS XL system with a 4GB SDHC card. All three cards came furnished with the systems, all three cards work flawlessly, and I even successfully transferred data between one of the 2GB SD cards, to the 4GB SDHC card during a system transfer, simply using a Windows 7 PC with a cheap no brand card reader.
The issue:
About three months back, I purchased a 32GB SDHC card when I was transferring my data from the 3DS system to the 3DS XL system. This card functioned swimmingly in the PC using the aforementioned no brand card reader. However, when I transferred my data to the card and installed it in the 3DS XL system, the card would randomly "disconnect" and all the visible icons stored on the card would disappear. Power cycling the system would cause the icons to return. When playing games stored on the 32GB SDHC card, the games would crash and additional card errors would appear. Following the advise of the Nintendo tech support forum and web entries, I formatted the card using SDFormatter V3.1, as well as followed the official step by step procedure provided in the web entry (however spartan it actually is). After several attempts, including multiple web searches and independent forums, I chalked it up to a bunk SDHC card.
Today, I thought I would give it a second go. I purchased a second 32GB SDHC card and I am currently going through the exact same song and dance as before, only this time the system only detects the card for a few seconds before flagging an error, rather than several minutes. I find it unlikely that I purchased two bad SDHC cards from two different electronic stores, even though both cards work without fault on my various PC and Linux systems.
Conclusion:
I would like to know Nintendo's default allocation sizes for the 2GB SD and 4GB SDHC cards, if these allocation sizes should change with the total size of the SD card (the allocation size changes the total size of the stored look up table), any other setup parameters that may affect opertion, which parameters to select using the SDFormatter (FULL(OverWrite) FORMAT, FORMAT SIZE ADJUSTMENT OFF/ON, ect. Look through nested options menus.), and which known SD card make and models don't work well with the 3DS systems. Basically, I am hoping for a fairly robust technical procedure to get a working 32GB card in my 3DS XL system containing the original data from the 4GB card.
I appreciate the help, and given the amount of research I put into this, I think a true technical response would greatly aid a multitude of individuals across the planet.