Actually, you should do a "Save Copy In" first... don't "save as" unless you want to permanently get rid of your unused files (which I highly advise against until something is long over). If you only do a "Save As" all it does is create a new Pro Tools file and it still references the same audio files in the Audio Files folder as your previous session and you will delete the files not appearing in the timeline.
When you do this "Save Copy In" (which is how you should/can actually create an exact duplicate of a session), choose "All Audio Files" to be copied with it. You may want to also check plug-in settings and some of the other options just in case you didn't print all your effects or mix elements down, especially if they're disregarding your 2.0 mix and will now be mixing for surround.
Then open that new session you created, once open hit Shift + CMD +U (mac) / Shift + Ctrl + U (PC) to select unused regions. Then Hit Shift + CMD/Ctrl + B to "Clear Selected". It will then ask you if you want to "remove from session" or permanently "Delete" from disk. When you select "Delete" hold down "option/alt" and it will prevent you from having to click "OK" over and over a million times. That will reduce your file size as much as it can be reduced.