Okay, so after having played the game a bit more to rack up some high scores and unlockable toys (Apparently I didn't play Touched all that much when I first bought it in 2014), and then thinking of how to do it the other way around, here's how to do it in reverse.
Presuming the use of FBI, Checkpoint, and of using Windows on your PC:
1) Open FBI, then go to TWL Nand → (accept the warning) → title → 00030004 → 5a324154 (if using the NA version; 5a324150 for the European version) → data, and copy the public.sav file to somewhere on your SD card.
2) Take out the SD card, then put it in your PC.
3) Go to [SD card]\3ds\Checkpoint\saves\AZWP WARIOTOUCHED, and make a new folder there. Do not use an existing one. (If the WARIOTOUCHED folder has a different four-letter code for its NA version, make the new folder there instead.)
4) Open the DSiWare public.sav file in WinImage
5) Choose to extract the backup.dat file that is inside it, to the folder that you made during step #3.
6) Rename the extracted file to WARIOTOUCHED.sav
7) Take out the SD card, then put it in your 3DS.
8) Turn on the 3DS, and open Checkpoint.
9) Ensure that WarioWare Touched is inserted in your 3DS's gamecart slot.
10) Go to the upper left entry (WARIOTOUCHED), and choose to restore from the folder that you made and named in step #3.
11) Start the retail version of WarioWare Touched, and the save will be used.
Visible side-effects on my end:
• Pyoro T, which I owned on the DSiWare version, had been removed, only for Orbulon's spaceship to drop it again upon entering the main menu. The high score for that game had been reset to 3000.
• Some of the other toys were marked as "NEW", which they weren't on DSiWare. Examples include Wario Paint, Piano, and Clacker.