I've never had an issue upgrading and it's a similar issue for me on my emuMMC as I just tried v15 and Atmosphère 1.4.0 (pre-release). I get a black screen when loading fusee.bin from TegraRcmGUI, black screen when chaining hekate, and then fusee.bin. I had payload=bootloader/payloads/fusee.bin set in the hekate_ipl.ini file and setting fss0=atmosphere/package3 for emuMMC in the hekate_ipl.ini file allowed it to boot. However, only my nsp installed games would launch and XCI installed games would fail to launch. I would get unable to start software for XCI installed games. I tried the sigpatches from that site (Build Hash: "-e580c3970"), I used your tool also, with the only difference being your tool creates a unique D0D4491814B562AF61ABD52E4BF0989405AF741A5C7C033AB3EB0EC8680AD98F.ips file, while that site has duplicate files like you posted above. I downgraded back to Firmware 14.1.2 (Rebootless Update), set my hekate_ipl.ini file back to payload=bootloader/payloads/fusee.bin, and everything works.