Yes, copyright law is complicated. You need to make sure the script used to create a deobfuscated binary isn't a derived work from the original binary, whatever that means (that's where consulting with a lawyer can help).
Is a patch a derived work from the file it applies to ? It is impossible to produce the patch without using the original file, yet intuitively, I would say no.
If I write a script that generates the Matrix movies from the binary file of, say, Elephant's Dream, I won't be allowed to distribute that.