JKSM VS 3DShell

I can't remember if this specific method also copies your save game for you, so if the save game doesn't appear on the digital copy, you can use Checkpoint or JKSM to copy your save game from the cartridge to the installed version. You won't lost your save data.

I assume based on your cfw comments you already backup your ds/3ds games, but for anyone googling or searching this reddit in the future... TWLSaveTool can backup your DS games. 3ds has Checkpoint or JKSM. You need homebrew or a cfw 3ds for these.

You can make saves for your games, in case you don't want to lose your progress, I used JKSM (Download here) there are some guides on the internet that can guide you. (Have these saved files in your pc, just in case)

yes I do this all the time using JKSM (https://github.com/J-D-K/JKSM)

If you still want the option though, you can hack your 3DS and use JKSM to delete save data.

That shouldn't be needed — old versions of 3DShell like 4.3.1 have a built-in FTP server, so any computer, tablet or smartphone can use a FTP program to transfer the games onto the 3DS. You just have to pay attention to which folders you're putting the files into.

You have to click 'Releases' on the page, which bring you to this page: https://github.com/joel16/3DShell/releases

3DShell to navigate the filesystem

There is also an homebrew app, Screenshot Merge, that merges the two images into one, adding black borders to the 4:3 bottom screen to adjust to the 5:3 top screen resulting in a single rectangular image, that can also be easily viewed as intended (top image on top screen and bottom image on bottom screen at the same time) on 3DShell - both apps can be found on Universal-Updater if you have it.

Most probably you downloaded the beta (v5.0.0), which does not have FTP support until the developer releases a stable version. Uninstall it and then install this version (4.3.1), which is the latest stable one.

Just in case this was a serious question, see https://github.com/joel16/3DShell