Are your NANDs unlinked? If so, then the only other thing that's coming to mind is the following idea:
1. Delete MenuHax payload. Rename CtrBootManager to auto.3dsx and HBL back to boot.3dsx. Edit boot.cfg accordingly.
2. Reinstall MenuHax to SysNAND via BrowserHax. Edit the MenuHax payload via NotePad++/HxD to replace all instances of boot.3dsx with auto.3dsx.
3. Use Luma3DS to install the
Homebrew Loader cia on EmuNAND.
4. Run MenuHax Manager while in EmuNAND. Hold X while selecting Delete to make sure that it would only delete the ext-data from the EmuNAND, if any is present.