Geoffers:
I don't see why one would need to submit a change to the FM to the NAA or AW - the normal and emergency procedures sections can be changed by operators. They are not limitations that must be obeyed.
If the operator's manual is subject to some other regulation (Part 135 in the US, for example) where the manual is a company document, then that's another matter.
I know of only one civil flight manual (and it's FW) where it says that only the procedures in this manual are to be used...