That sucks. I used the Wifi backup tool to take the Save from an original Zelda PH cart, converted the save using the r4 conversion tool, then just named it the same as a rom I obtained elsewhere and it worked fine.
Hrm....I wonder if R4 commander has the ability to check the roms...although my entire library (about 350 NDS roms...shhh) was recognized by R4C including release number and game title...
Ahh well. In computer programming our professors gripe about future engineers not taking chances and fixing...