Why are there two copies of the encoded video? Why can't DCP-o-matic delete one when it has finished?

You will see that, after a completed encode run, the DCP contains a large video MXF file. There will be another large MXF file within the video subdirectory. However, these are hard links. It appears that there are two large files, but in fact there is only one large file with two different names. If you delete one, you will see that the free space on your drive does not change; the two files actually only take up the space of one (though Windows will often say otherwise if you count the size of both together).

The exception to this is if you are using:

In those cases you will have two copies of the video file.