You can extract coloured chunks or sections into a new Audio Notetaker tab or a file you already have open, by clicking on the Extract Button on the Toolbar.

You can choose to Extract Audio or Extract Sections and you can also choose to re-order the new project according to your section colours.

Using the drop down list at the top you can choose whether to extract to a new project or one you already have open. The extracted sections will be added to the end of an open project.
 

You can select which colours you want to extract. The whole section contents (Images, Reference and Text Panes) will be copied along with the coloured chunks/sections.
 

Selecting the Reorder Using Section Colour check box will re-order your document according to the section colours you have used. Your sections will be in the order that the colours appear in your colour key.