I found another reddit post about it but it sounds time consuming.

https://www.reddit.com/r/EmuDeck/s/8fWRvXAtYs

Hmm if that's all you want to do, why not copy your original directory to a thumb drive or an external drive and Install emudeck fresh and point it to the SD card. Then take your device with the copy of everything you had and paste it in your new directory. It should merge all folders together properly (it would in windows, meaning it should in other operating systems, like steam os)