Editing involving several backup drives: how to assemble a project with minimal clip duplication? This question might be a little complex, but here's the situation:

We are a small team and we shoot almost every day, we do correspondence-type shooting. We are backing up our footage to external encrypted drives, there are three now. When I edit, I pull the folders that I want in the edit from the backup drive onto my Editing SSD drive. Because we shoot in MXF and MTS, I usually then transcode everything to ProRes. After that, I delete the original MXFs and MTS' to conserve space.

With this, I end up with duplicated clips on my editing drive. When I edit in Final Cut Pro X, I choose several clips from these folders to be in the final edit from inside the FCPX, and after I render, there are unused, but linked files left behind. I have no way to automatically delete what was not used, and I don't want to delete the folders with transcoded footage if I were to revise the project at a later date.

Is there any way to delete files not used in the timeline? How do I conserve on space? Is there anything in my workflow that could be optimized?
I am not sure why you end up with duplicates. However you might be interested in having a look at the proxy workflow from Felipe. It probably can help you to get rid of duplicates and conserve space.