If you already have a flashed ntrboot flashcart then just install it with ntrboot (https://3ds.guide/installing-boot9strap-(ntrboot)) then backup your tickets, do a system transfer, and restore the tickets (or run tikShop).
If you don't have a cart already, then do the DSiWare hax method. https://3ds.guide/installing-boot9strap-(dsiware-game-injection). Afterwards restore the pre-transfer NAND backup and extract the tickets, and inject them on the target console (or run tikShop) to make the games show up again.
Thank you for the response, by the time I read your post, I already hacked my N2DSXL with my flashed ntrboot flashcart and started messing with Freeshop and ran into some problems however.
After installing Freeshop and updating it, I tried to re-download all of my games from my O3DS to my N2DSXL and had 24 downloads going at once. However, whenever I try to exit the Freeshop app, the app crashes giving me this screen: https://i.imgur.com/qdTv3al.jpg
Even when I try to reset my N2DSXL and enter Freeshop again, I am greeted with the same crash and on home menu, I have a few game downloads paused at 0% but I don't understand how to delete them. Is this happening because I tried to download too much at once? I would upload my crash file, but gbatemp won't let me upload the .dmp extension. Any advice would be greatly appreciated. Is it too late to try the system transfer Quantumcat mentioned? And what exactly are tickets? I have all my files from my hacked O3DS backed up on my PC if that helps. Thank you for your time.