When you convert Noise bins the representation of noise is converted into a sampled signal and added to the ‘Signal’. After this operation it impossible to extract the noise.
Try this:
Place a fork component after your EDFA and on both forks use a “Signal Processing Library/Tools/Optical/Signal Type Selector” component. You can set one to Sampled signals and one to Noise bins. After the selector you can convert the Noise bins signal to a sampled signal with the Convert to Sampled Signals component and that should create to signals of equal length that represent the signal and the noise.
Cheers!