If you import audio clips from another project that are currently in the Trash of the active project (using Copy/Paste or ‘Import Tracks from Project’), Nuendo does not move these files from the Trash Pool to the Audio Pool when placing them onto the timeline. As a result, even if you run ‘Media > Prepare Archive’ and run ‘Trash > Empty Trash > Remove from Pool’, Nuendo deletes the active clips from the timeline.
Martin