Topic: Transfer purchases

I used to share a 3ds with my sister but i'm getting a new one for Christmas and wondering if i will be able to get the games we had downloaded from the eshop on my 3ds as well? Would system transfer work even though i just want the games?

Well a system transfer will only move games. You cannot copy them

In order words, you must either start in a blank state or leave your sister without any digital games.

Basically what @WaLzgi said. If you do a transfer you will move all the games from the 3DS you shared to your new one meaning that the old 3DS will be wiped clean with nothing on it. And you can only transfer everything you cannot pick and choose in case some games were yours and some were hers. So in other words you are going to have to rebuy the games again if you want them on another system.