Is it possible to transfer your town from a physical copy of the game to the digital copy

As the 3DS does not save cartidge save data to the system or SD card, there will be no clash between the two instances. They will be treated as separate games, with one file being on your download instance, and one on your cartridge.

StreetPass and SpotPass hits should go to both copies. Nintendo has fairly recently made available a tool to move save data from cartridge to download versions (albeit not the other way), so if you'd ever feel the need to do that it's completely possible.

Animal Crossing wouldn't allow that if you've been playing Animal Crossing since your backup. If you backed up your file 6 months ago, but then you kept playing, Animal Crossing won't recognize the old data anymore.

The problem is that Animal Crossing really doesn't like cheating, which is why they penalize you for time traveling (and they prevent you from trading bugs and fish, I'm pretty sure). Another thing Animal Crossing doesn't really like is when you cheat using multiple files. So they have a way to prevent that for digital downloads. You could all it "Last Play Save".

Using that system, Animal Crossing won't boot data that's different from the last play's save unless you're starting a new file. So, you can do this:

• Create file with user Crazy Redd
• Play file
• Create file with user Crazy Steve
• Play file

But you can't do this:

• Create file with user Crazy Redd
• Play file
• Copy file data to computer, delete from SD Card/Use new SD card
• Create file with user Crazy Steve
• Play file
• Copy file data to computer and switch with Crazy Redd data/Use old SD with Crazy Redd data
• Play file

The "Last Play Save" would stop you from playing the Crazy Redd data. (Also, if you create a new file, Animal Crossing will delete old data, just FYI) That is, Animal Crossing is looking for the Crazy Steve data, so it won't look for (or run) the Crazy Redd data.

This has a timestamp as well. If your last play save was yesterday, but you have a backed up copy of your file from two months ago, the two month old data won't run. Animal Crossing will always run the last play save only.

If you're just switching cards and you don't plan on playing a new game in between or you don't plan on trying to reload old data, you're fine, though. For references, here's someone who didn't know about last play save and here's a (super) brief thread about changing SD cards (the only part that has anything to do with Animal Crossing is the last line of the answer).

Will you mess things up by trying to load the old data? No. Animal Crossing legit won't play your old data anymore. It will be looking for the last play's data and when it doesn't find it, it's not going to run your old data... it's going to ask if you want to delete the last save and make a new file. If I were you, I still wouldn't try it, though.