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Unfortunately not. You may only customize and save your default Swatch to be available across all documents by default.
Multiple Swatches/folders option is provided to let you organize (or restrict) the colors for a given project only and gets saved for corresponding project .
You may wish to try out new workflows using the Kuler Panel (that lets you reuse themes) as explained here: Flash Professional Help | Working with Kuler Panel
If you'd like to make any suggestions, post them here: Adobe - Feature Request/Bug Report Form
Why have the folder option if it's exclusive to a specific document?
I don't understand the logic of removing the feature where you could save different swatches.
Every project I work on for clients have a different colour theme. In the old Flash, you could create your theme or swatch, save it and import it into any flash file which was extremely useful.
Having to add and change the default swatches, thereby either having to remove one project's colours or making it a massive swatch panel with more colours than you need seems a step backwards. And when I try create this new "theme library" I have to save 16 themes to a library? I really don't understand why this is.
All I want to do is save a dozen or so colours out to their own swatch library so that I can import these into my project files for each client.
Is there really no way to do this?