I think with this particular 3DS title, there may not be much value in having the digital version on your system. The physical 3DS version still holds some value especially if it is the version with the box and soundtrack. There are some games out there in which the physical copies increase in value once the digital version is pulled, but this is a unique scenario where there is another version on a newer system, so it hasn't increased the value. I wonder if the reasoning behind it getting pulled is that Nicalus has the publishing rights to the game now?