Can saves be used back and forth?

Just a general question I wanted to ask before doing all the work of getting this set up and dumping my AC:NL cartridge. Can the saves be safely decompiled for the emulator and then recompiled for the 3DS?

Thanks!

Yes, you can transfer saves between Citra and your 3DS.

Does that include the cartridge-based saves? As in, I can move a save into and out of it? Or would I need to get the digital copy as well?

Also, where should I look for instructions on how to do this? The FAQ goes over the process of decompiling but doesn’t really explain the reverse process.

The reverse process would be:

Open the save data location by right-clicking on a game in the list in Citra and selecting “Open Save Data Location”.

Now copy the all the files and replace all the files that you have made with the Export Save option in JKSM in the SD card.

Now go into JKSM on your 3DS, select SD/CIA, select your game name, select Save Data Options, select Import Save, and finally select the name that you created for your folder in the SD card.