DCP-o-matic should probably prompt you for the location of all missing materials when you load a folder linking to missing material and, if "Cancel" is clicked, should replace materials with black, audio-less footage.

This will require:
a) the ability to just make up blank footage of specified sizes and lengths (similar to the static image feature, with a built-in black image)
b) the ability to swap out material for other material without changing crop/sizing attributes if possible