I'm a noob at homebrew and wii code in general, but I recently downloaded Homebrew and Bootmii for 4.3U.
I have 2 SD cards (at least I thought it worked this way). One is 1 GB and one is 8 GB. The 1 GB one contained all of my virtual console and wiiware games, as well as the Smash Bros hack: Project M. The other had the rest of my homebrew data. Everything worked alright (even project M!), however the other day, I went to play some VC games and the wii couldn't find any data or channels on the card. I backed up both cards and copied all of the data from the 1 GB card to the 8 GB, and it still doesn't work.
By the way, the 1 GB card is formatted to FAT. Does it need another format to work with a modded wii? Or does my Wii think the virtual console titles are from a separate wii (pre-modding)? Any advice would help! . Oh and also, Project M works regardless, which means that the SD card is being read by the Wii, the channels for the VC and Wiiware just aren't appearing .
If the Wii Shop data wasn't wiped, if these are legitimately purchased items that you no longer have access to, you can always redownload them for free, storing them on the SD card again to be playable from the SD Card Menu.
If the Wii Shop data was somehow wiped, you would have to repurchase the items as you no longer have the rights to play them.
And if you followed my if-then logic, there is one other case left. If you fall into this last case, we can't help you since we do not support piracy.