saynomoo/mongo-java-driver — comment on commit 28ec11aa7add0ff5f5afce82c6a042b0219e2cc0
File:  line 0
By scotthernandez:

Seems reasonable but for now I would suggest searching for the files by their metadata, then deleting them and then deleting the chunks by
file_id, using $in. Let me know if that makes sense.

I have created a jira issue to track this change and schedule integration for a release: http://jira.mongodb.org/browse/JAVA-475