Yeah that's the thing i uninstalled the none system apps from nand and now do you have any idea how to delete the black apps ?? i put them in a folder and tried to delete them but it says it contains data that cannot be deleted
So you've already removed the wrong apps from NAND but those are still there?
If thus i would suggest you to do so:
0.If you always play games on EmuNAND, and games are large you can easily identify the EmuNAND for SD:/Nintendo 3DS/Hash/Hash.
1.Open FBI. Turn to "Launch Title" Mode. Now a title list appears. Take a piece of paper and your pen/pencil, you would have to record something.
2.Write down every titleid of SD titles you've seen onto the paper. After each one is recorded, just arrow-down to the next till no more.
3.Exit FBI. Shutdown 3DS.
4.Now open your SD card, say, SD:/Nintendo 3DS/Hash/Hash you've identified in step 0.
5.In "title" folder, there is lots of folders. I would only tell you a titleid 0004000000164400 matches the folder title/00040000/00164400.
6.So you open the folders and checkout the names to find out which isn't in the titleid list you've written on the paper.
7.Once these titles are found, You can simply move the corresponding folder out of SD (to PC). I mean 00164400 folder in 00040000 not the whole 00040000.
8.When you've finished that. Stick your SD back into 3ds, and go to emunand. See if the black square is still there.
This solution is to the wrong SD files. Sometime you might backup the SD card. However your backup might contains titles that you've uninstalled before.
When this type of problem happens on a Linked EmuNAND.. Plug out your SD and do System Format in SysNAND and do CFW setup.
THat means you may have some games in SysNAND but these isn't in your EmuNAND. However in this case you should have seen Black Squares without GW (OFW).
If there is no such app. You wouldn't have to move any folder out of SD. And in such situation, sorry i can not help you further more.
And to say. To remove a title (delete app) from NAND you can only use FBI or your own source code that uses am:u. It wouldn't help if you put those in folder and..Orz