Akarutheyoshi is right, only by calling Nintendo can you have them change the eShop rules so that this purchased DSiWare game can be redeemed for the same game on the eShop (but any saved data with be lost, you are right that it cannot be transferred).  In answer to your other question, Nintendo does not plan to release a firmware update that will allow DSiWare games to be downloaded onto an SD Card in a 3DS instead of directly into the System Memory.  This is due to a basic technical limitation.  The original DSiWare games, before the release of the 3DS, were formatted by Nintendo to be on the DSi System Memory.  Since the DSi did not use an SD Card then, they cannot be used on an SD Card now.  I suspect that the inability to put DSiWare on SD Cards is due to piracy concerns.  It is unlikely that a firmware update will be released in the future that will allow DSiWare games to be on an SD Card.  For now, we must be content with putting our DSiWare in the 3DS System Memory.

Sure you can, but just not Art Academy.  Sorry for the long winded reply.

-Thanks

MARIO  wrote:

 

I believe the Art Academy titles have been added to the list of titles that can be transferred. You can find information on transferring titles, including a list of titles that cannot be transferred, here (click here.) If the original poster still has these titles on their DSi, they may be able to redownload the transfer tool and try again.

Mario, you are correct.  I just transferred Art Academy 1st Semester from my DSiXL to my 3DS.