3DS to New 3DS - Pokemon Omega Ruby Corrupted Save

I just upgraded from a 3DS XL to a New 3DS XL and have encountered a major issue.

What I've done:

1. Completed a wireless transfer from the Old 3DS to the New 3DS, which brought my E Shop account info over.
2. Put the SD card from the Old 3DS into my PC and copied all the contents onto my hard drive.
3. Put the Micro SD card from the New 3DS into my PC and copied all the contents from the old SD card onto the new one.
4. Booted up the New 3DS. All of my downloaded content and game-saves are intact, except Pokemon Omega Ruby.

When I boot into Omega Ruby, I get the following message:

• The saved data is not compatible with this version, so it can't be used. Refer to the electronics manual for details. (Ver. 1.2)

When I boot into Pokemon Bank (paid $5 for access because I thought it might work), it sees my game-save, but when I try to access it I get the following message:

• The saved data in this software does not match the previous saved data. It cannot be used.

I've contact Nintendo twice, and neither of the support reps could offer any advice besides wiping my save and starting over (which is not an option).