This seems to be a relatively common problem. As I've said in previous threads, I've never heard of this problem before GW3.0 and up. I lost my 30 hour Persona Q save to the exact same thing. MH4U (eshop/cia version if you have that one) can be backuped via SaveDataFiler, and the 3ds/3dz version is the usual GW style .sav. Take backups ALWAYS as it is more sour to lose the save completely, than just lose a few hours of progress.
Personally, I've started taking constant backups after Persona Q was corrupted. I've made a very simple script for myself that automatically backs up all savefiles on the SD card to my HDD, that way I don't have to do it manually. So if I put in the SD card on my computer it'll make a folder marked with a date and copy all .sav files and the SaveDataFiler folder into it.
If there are any OS X users out there who wants it, here's the script. Just edit it with your own backup path and username and add it to ~/Library/LaunchAgents and the other one to ~/Library/Scripts/ and it'll automatically backup the 3DS' SD card when you insert it into your computer. It'll only work on OS X though, so if you use GNU/Linux I guess there are similar ways to do it using rsync and Windows probably have some sort of program to do it or something.
thanks for the script.
Now that we have some Homebrew I hope soon someone create a app that will backup all saves to so folder on the SD, it'd would be great