I mentioned in another thread that this is the most sensible way to handle this, because there's no way of knowing whether some of the links to identical/deduplicated files were legitimate. My previous comment: http://news.ycombinator.com/item?id=3489054
Right now the law says that a service provider must take down or block access to the material. Taking down only links (whether they're HTTP links, or pointers in a software app, etc) pointing to the material does not meet that requirement -- the material is still there, and it's still accessible through the other links.
So while it would be sensible to only remove the one link that you were notified of, if there are others, then by not taking them all down the service provider does not gain the safe harbor protection of the DMCA and remains liable for copyright infringement. Right now, as a non-lawyer reading the DMCA, it looks to me like any storage service that dedupes files is required to remove the file (from everyone's account) when any link to that file is reported, even if the other accounts have permission to store that file.
I feel like this should probably be a grey area to be sorted out in court, if not a reasonable codification into law.
But as I understand it the wording of the DMCA can be interpreted to mean that you must remove all links to the file, regardless of whether or not some of those users had the legal right to distribute while others didn't.
I mentioned in another thread that this is the most sensible way to handle this, because there's no way of knowing whether some of the links to identical/deduplicated files were legitimate. My previous comment: http://news.ycombinator.com/item?id=3489054