I am running into the same problem Neutral0. I'm on 6.2 on my emunand when i installed sx os 2.5.1 it wont recognize my nsp's that i had installed prior to going to 2.5.1 beta sx os.
Edit: I think i might have found our answer. This is from the gba temp forums From user Thaikoa
"TX might not test and experience enough about linking nands when creating emunand. And there doesn't have any well guide or user's manual from them yet and won't have to.
The reason why your installed games on emunand has randomly archived is that when creating emunand, the two nands share the same Nintendo folder which is the same hash, encryption or something like that. The two nands won't share the same ticketblob, so that when emunand installed more games than sysnand or vise versa when booting sysnand without those installed games on its ticketblob, all installed games on emunand will be wiped out completely.
TX might not test and experience enough about linking nands when creating emunand. And there doesn't have any well guide or user's manual from them yet and won't have to.
The reason why your installed games on emunand has randomly archived is that when creating emunand, the two nands share the same Nintendo folder which is the same hash, encryption or something like that. The two nands won't share the same ticketblob, so that when emunand installed more games than sysnand or vise versa when booting sysnand without those installed games on its ticketblob, all installed games on emunand will be wiped out completely."