Massive Independent audio file project files

Ive been mixing a feature film in soundtrack. Previously I had a file containing the full film and (because I couldent get an OMF from avid to work no matter what i tried, so much for the bloody open media file format...) I had a straight wav of all the films audio.
I had gone threw the whole film like this chopping up the wav inserting wildtracks ect. I realised as I was trying to add foley that this set up would not do.
So I opned the movie file in Final Cut and chopped into into individual scenes. Sent Scene 1 to soundtrack I then copyed the audio i had already worked on for that scene into the project.
I was very happy with this untill i saved it, and i took a REALLY long time.
Investigating the media folder I found that three or four .stap files all contained the full wav of all the films audio. Around 800mb worth. I tried replacing with an independent audio project but it kept the same full 800mb file.
According to the manual replacing the file with an independant audio project should have trimmed all the unnecasery audio? Whats going on?
Please help, I cant go on making several 800mb files for each scene but I can bring myself to do it all over again! Thanks in advance.

I don't believe you can. FCP sends the entire file, not just the in to outs.

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