Troy I could be wrong on this but I don't believe the files section in Boxer actually stores the files but more so acts as a quick link back to the actual attachment. I believe in order to delete the file you would need to actually delete the email its associated with.
Thank you for this answer. That is exactly what it is. I made an assumption that the file was stored someplace in the Boxer app but did not realize it was just a ink to the attachment in an email.