This issue hit me as well. Not only does replacing boot0/boot1 not work regardless of where I get it, even creating a completely new emuNAND doesn't work as I detailed
here. They really should have updated their release notes to tell people that it's incompatible with 6x at the moment and, of course, a way to move it back to sysNAND since apparently even those who got it to work found it to be buggy.
The good news is that my emuNAND will probably work whenever they fix it. The bad news is that I neglected to make a backup of my NAND right before doing this so the only way for me to play backups is to not only roll back to 2.0.1, but create a new emuNAND on sysNAND and then using Checkpoint to restore them in. Not ideal.
Another issue with their new emuNAND is that you can only create a 32 GB one (no option for smaller or larger), but cannot expand an existing emuNAND to 32 GB. In all likelihood, I will probably end up using a second emuNAND and then will have to use checkpoint to backup my saves and restore to the old emuNAND and then if they don't implement a way to expand the emuNAND I will have to create yet another emuNAND, and use checkpoint to move all the saves over. Ugh. They really made a mess of this.
I just tried this and it doesn't work for me. It doesn't matter if I get these files from a new NAND dump, an old NAND dump, or from creating a new emuNAND. It also doesn't matter if these files are placed in my old 15 GB emuNAND created in SX OS 2.0.1 or in the new 32 GB emuNAND created in SX OS 2.3.
OFW and CFW both at 6.0.1