Do game cards and digital copies have separate saves

You can not have multiple save files of individual towns on the same 3DS system.

Every time you save your game it generates a new, random "Save ID" and stores that ID in both the SD/Savegame and the 3DS's system memory. Trying to load a save with mismatched IDs will result in being forced to wipe the save.

This prevents two things:

1. Having two towns with one copy of the game by using two SD cards.
2. Reverting to an older backed up save to undo changes you aren't happy with.

http://gbatemp.net/threads/question-about-id-checks-with-3ds-and-new-leaf-save-files.349216/

I have personally tested this (having purchased a 3DS and transferring to 3DSXL- my game was cleared since the save data and the system ID did not match). Prior to this, we attempted backing up the SD data, erasing it from the SD and attempted a new save file on the same digital copy. This also resulted in the ID conflict. I have contacted Nintendo on this matter causing an inability to back up data. I am yet to hear a followup reply.

In the case of mismatched IDs, the game will load with a "corrupted data" error. This forces the system to erase any save data associated with the digital download- and any backed up save file will no longer work for AC:NL.

Go to the eshop and download the save data transfer tool app. you can use the app to move the save. The save on the cart will be deleted.

Here is the official page:http://www.nintendo.com/consumer/systems/3ds/en_la/gi_index.jsp?menu=save_data_transfer&submenu=ctr-gi-app-save-data-tool-overview