I see that it has been a few days since the last reply, but in case anyone else takes a look at this, maybe I can be of some help...
I'm in the prepress department at a print shop which runs almost entirely 2-color jobs. I think that maybe what the printer in this case was trying to ask was for yuendos to keep the image in CMYK mode, but delete all information in 2 of the 4 channels; so that when they printed separations, the only 2 channels used in the document would be the only 2 plates. I have occasionally asked customers to do this if I thought that trying to explain how to make 2 individual grayscale (or bitmap) tif files for each color plate would be too confusing. I have also had to do this for some customer files given to me once in a while. It's not a very pretty way to do things, but it works in a pinch.
As far as duotone is concerned, it's not the only (or best) option for 2-color printing. It really depends on the job because a duotone makes for very tight registration, which usually means higher price tag! So ask your printer before giving them a duotone file.