OK, now I have a completely unrelated problem.
BotW from JNUSTool:
9.82 GB in 260 files. Installs perfectly.
BotW, the above .app files decrypted with Cdecrypt with two folders renamed, then repacked with NUSPacker:
9.79 GB in 27 files. Fails to install, error code 0xFFFBFFFB.
I don't understand why this is so. The 0000000A.app, 0000000B.app, 0000000C.app and 0000000D.app contain almost all the data, being around 3GBs each, but this isn't so in the real files. As I said, the only thing I changed are the names of two folders, so there shouldn't be a huge difference. It's always possible that Cdecrypt is spitting up wrong "meta", "code" and "content" folders from the JNUSTool files, and it's not NUSPacker's fault.