Why do you want to use old DLL with new executable? In general it's a bad idea.
Normally I would suggest Mono.Cecil, as it can add new functions to assembly. But taken into account your previous question:
I doubt that it will work because Mono.Cecil cannot handle mixed-mode assemblies.
a) patch main exe so that it doesn't require IsSecondInstance and use old DLL or;
b) patch new DLL like normal people do.