You'll more then likely need to update both hekate and atmosphere to the latest version. I've had a few odd issues with it, and usually just re-updating atmosphere and hekate fixes the issue for me. If that doesn't fix it, i'd suggest backing up the whole sd card and starting from scratch to see if that fixes it, then copy the Nintendo folder back to the SD card, along with the folder for EMMC if your using a file based configuration. If your using a Partition based setup, however, i'd suggest just backing up the readable partition and starting that from scratch like previously stated. I like to keep my updates of hekate and atmosphere in sync, as sometimes version differences between them can cause issues.
Ex. only updating atmosphere and not hekate can cause decryption errors, if i recall correctly.
