We don't restrict you from importing footage from disk multiple times, because there may be circumstances where you want to have different footage settings for the same clip (for example, if you have a very long clip and you want different start/end frames for multiple subclips). This is why replacing one clip does not necessarily replace all of them, and also why we don't automatically show only one footage operator for duplicate clips.
However, the basic situation here is more about what happens when you duplicate or copy/paste layers in a composite. In combustion, importing footage multiple times will create separate footage operators for that footage, as does duplicating layers, causing the situation you describe where you have many duplicates of the same footage. If you want many layers to reference one footage operator, you should use the "New Layer from Operator" command, found in the Object menu, instead. This lets you create a layer that references an existing operator, in this case you would just double-click on the footage. Now, you don't add an additional copy of the footage operator to the workspace, the footage is "branched" into two layers, or more. This command can work on any operator, for example you could have a clip with a keyer, use new layer from operator on the keyer, and have multiple layers derived from the same key, and each could have additional operators applied to it independently.
If you've already built a workspace that has many copies of the same footage because you've duplicated layers, you'll have to "merge" these together. There isn't a single command to do this (it is on our to-do list), but you can use the New Layer from Operator command to create references, copy/paste the keyframes and attributes from the old layer to the new, then delete the old layer.
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Greg Niles
combustion Product Specialist
Discreet