All cut-and-pastes will leave tracks at their full 3 hour length, even in a new project, regardless of how long it ‘appears’ in each song. Certainly, that would take up a lot of disk space on the project drive and where you back them up to.
As far as I can see, I would approach it in this way:
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Save the master project, to have something to pinch from when necessary.
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For each song:
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2.1 Set up the markers.
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2.2 For each track:
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- 2.2.1 Export to a separate file, not importing into the project, but naming so you can identify each song and track for use at step 5.2.1.
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Save the master project to another project folder.
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In the CLONED project:
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4.1 Setup group and FX tracks.
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4.2 Insert FX to be used on every track.
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4.3 Set levels and FX parameters to ballpark values.
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4.4 Remove all audio clips, but leave the audio tracks themselves.
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4.5 Delete files in the Pool.
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4.6 Save the project, just-in-case.
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4.7 Save as a template.
- For each song:
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5.1 Using the template from 4.7, create a new project into its own folder.
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5.2 For each track:
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- 5.2.1 Drag and drop the audio file exported at 2.2.1 to the start of the track.
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5.3 Save the project.
- Mix each project independently.