I've run into a problem. When I use DotNet.3DS.Toolkit.v1.4.6 to build my changes into a CIA file, I get a warning saying that HeaderNCCH6.bin, HeaderNCCH2.bin, and LogoLZ.bin are missing. I believe this is the cause of the random crashes I've discussed earlier here. For some reason the crashes at the end of chapters occur on my 2DS, but not on Citra. Perhaps the emulator doesn't use the missing files and an actual 2DS does?
I've attempted to solve this by extracting roms from many different sources to find the files, but to no success. How do I get the missing files?
I'd really appreciate some insight on the proper methods and tools to extract and rebuild ROMs. HackingToolkit 9DS V9, HackingToolkit 9DS V12, and DotNet.3DS.Toolkit.v1.4.6 each get me different results when extracting the same ROM, which is very confusing.