That will happen because your SysNAND and EmuNAND are linked. In other words, they share the same exact
Nintendo 3DS folder.
- Nintendo 3DS/<ID0>/<ID1>/...
As for why some some games are recognized by both SysNAND and EmuNAND, you probably installed a set of games on one XxxNAND and then used or copied making that into the other XxxNAND. Anytime you switch from one to the other, that NAND will notice something has changed in those titles and update its HOME Menu icon cache. In order words, that switched NAND will assume those tampered titles are new installs.
If you want to quickly unwrap multiple HOME Menu titles, use
Cthulhu.
***
You can update either SysNAND, EmuNAND, or both to 11.8.0-41E.
It's generally recommended you ditch your EmuNAND. To do this,
- Backup all your EmuNAND game saves + extdata with Checkpoint or JKSM.
- You should backup titles found on SysNAND while you're at it.
- Dump all your EmuNAND titles [games / DLCs / updates] as *.cia with GodMode9.
- GodMode9 Usage - Dumping a Title
- For EmuNAND, instead of [A:] SYSNAND SD, look in [B:] EMUNAND SD.
- You may need to manually/selectively backup titles that are from EmuNAND.
- Copy all the stuff on your SD card onto a computer.
- Using MiniTool Partition Wizard (free edition), delete the EmuNAND by merging the SD card's partitions into one. Reformat the card with these settings:
- Partition: Primary
- Disk: MBR
- File System: FAT32
- Cluster size: 32 KB
- For further instructions on how to use this software, read this post.
- To ensure your SD card isn't faulty or fake, it's best to check while it's empty with a Full Write + Verify Test in H2testw.
- I advise you don't skip this step if you've never used H2testw on that SD card.
- If it passes the test, delete the *.h2w test files.
- If at any moment an error is reported, stop the test. You need to replace the card; it can't be fixed. Go back to step 3 or 4.
- Copy all your stuff back onto the card.
- From post #16 above, update your custom firmware to Luma3DS v9.1, boot9strap v1.3, and GodMode9 v1.7.1. Then, update your 3DS firmware to Sys 11.8.0-41E.
- There are two parts to your custom firmware: SD card and CTRNAND. You need to update both.
- Update the custom firmware first before updating the 3DS firmware.
- Reinstall all your *.cia titles that was originally from your EmuNAND with FBI.
- Restore the saves and extdata for those games with whichever save manager you used.