About duplicating and deleting media files
When you delete a layer in the Layer’s list, by default Motion deletes the corresponding media item in the Media list (but does not delete the source media on your computer or connected storage device). If you want to delete a layer, but retain its source media item in the Media list for future use, open Motion Preferences and, in the General pane, deselect the “Automatically manage unused media” checkbox. For more information, see General preferences.
When you duplicate a layer in the Layers list, a new instance of the source media is created in the Layers list—however, no new source item is created in the Media list. In a project with duplicated layers, you can adjust the attributes of all duplicates simultaneously by adjusting the source media’s parameters in the Media Inspector (see Display the Media Inspector).
If you’ve duplicated layers and want to delete them all at the same time, delete the corresponding media item in the Media list.