Oh¡ keeping your installed games on your sysNAND¿ let me think...
Hmmn... Apparently it's not possible like that... To get those games recognized by a NAND, you need the movable.seed, wich will "link" your NANDs and show the unwrapped bug, and to show the games on N3DS Folder you need the ticket.db with the tickets of those games... And another folder called "dbs" contained on N3DS Folder too... So, maybe you can try to extract seed.bin from emuNAND, and the 3 Folders under your second randomnumber Folder, then format emuNAND, het to home menu and inject ticket.db, then copy those 3 folders to the same place on your new N3DS folder... I don' t think it will work, but you can try, and I hope that you understand this...