Roger,
I'm sorry to hear what happened (yeah, maybe you shouldn't test the larger roms anymore).
So the SD card works fine otherwise, but it's not detected by the menu .4 anymore, right ?? You can press 'B' and then 'A' to re-detect (do that several times) to verify
Have you tried defragmenting the card, and re-formatting in windows (using both fat and fat32). My SD card got messed up before and the menu wouldn't recognize it, but a fat reformat on my pc fixed that...
Maybe you should start again from scratch (delete everything on the sd card, reformat it, re-flash the menu onto the flashcart, etc)
Lemme know how this turns out since I haven't heard of any other problems like this caused by flashing to the cart...
BruceG