Whoah. DON'T go into the System Transfer settings though! I was previously out of system transfers, but since they removed the limit, I opened the settings to see if it would actually let me do a transfer.
Without asking me, it just started the transfer process, by first deleting all the installed downloadable software, then confirming that DSiWare would be moved to the SD card. I didn't want it to do that so I turned off my 3DS and when I turned it back on, that's when I saw that all my stuff had been deleted.
I can't log onto the eShop right now to redownload anything (I get an error code) and I can't even use the StreetPass Mii Plaza since the update file it needed had been deleted. I get an error when I try to redownload that, too.