Basically, I've tried looking into this question myself and wasn't able to find a confirmed answer.
I have my current 3DS system, which has a 4GB SD card. I have bought several games from the eShop, but the SD card is too small to fit all of them at once; as such, I've been deleting games that I'm not currently playing to make room for others for the time being, knowing I'll be able to re-download them later.
However, I got a New 3DS XL and a 32GB microSD card. If I were to perform a system transfer between the two consoles, would I be able to re-download my deleted games from the eShop from the new console? Or would I somehow need to have all my games downloaded at once before the transfer?
Best Answer
What to Do:
Source System
From the HOME Menu tap the System Settings Icon and then "Open." Tap "Other Settings." Tap "3" and then "System Transfer." Tap "Transfer from Nintendo 3DS." Read the information about the transfer and tap "Agree." Tap "Send from This System." If you have linked a Nintendo Network ID press "Next" and use the on-screen keyboard to enter your Nintendo Network ID password.
Target System
From the HOME Menu tap the System Settings Icon and then "Open." Tap "Other Settings." Tap "3" and then "System Transfer." Tap "Transfer from Nintendo 3DS." Read the information about the transfer and tap "Agree" Tap "Receive from Nintendo 3DS."
Source System
Select the system that will receive the transfer.
Target System
Tap "Yes" to accept the transfer.
Source System
Read the transfer information and tap "Next" to continue. Tap "Yes" to confirm. Tap the blue "Transfer" button to continue.
Target System
Tap "Delete" to confirm deletion of all Nintendo 3DS data on the target system's SD Card. Tap the blue "Delete" button to begin the transfer. If "Do Not Delete" is selected, the Target system will request to perform the transfer without deleting the Nintendo 3DS data on the SD Card. Tap "Yes" to begin the transfer. No matter which option is selected, you will need to redownload any preinstalled titles on the target system once the transfer has been completed. When the transfer is complete, tap "OK" to restart the system.
Source System
Remove the SD Card from the source system as it will now be used in the target system. If the target system has a higher capacity SD Card than the source system, you may choose to transfer your content to the higher capacity SD Card instead.
Source: http://en-americas-support.nintendo.com/app/answers/detail/a_id/227/~/how-to-transfer-content-between-nintendo-3ds,-nintendo-3ds-xl,-and-nintendo-2ds