But surely the compiler (assuming a compiler is used) would convert the new high level language into regular Scheme primitives - I think it's unlikely that the result wouldn't be identifiable.
No... the product allows you to write scripts to manipulate its machine code IR database in scheme, and then spit out the machine code as nasm assembly, assembly them, and then run the appropriate linker in the same way that was used to produce the original exe. Scheme is used as a macro language. So you use scheme to say: change the code at EA 0xdeadbeef from a mov to a jmp. You can reorder functions, insert and remove code, etc. It works because it has very high quality disassembly based on observing compiler and linker invocations and introspecting the artifacts involved.
Ahh, that makes more sense, I thought it meant simply creating a higher level language from Scheme rather than manipulating the last stage(s) of producing the binary.