The alleged libel is based, in part, upon Funnyjunk's claim that they are acting legally within the safe harbor provisions of the DMCA by only hosting UGC and taking it down upon notice of infringement.
The Oatmeal's response to the claim included a list of content infringing his copyright. Funnyjunk is going to want to remove that content to retain its safe harbor from liability for the infringement. It may or may not be a properly worded notice under the DMCA, but a lot of notices UGC hosts get aren't, and they still take down the content -- because the intent of the parties and whether they acted in good faith matters when it's time to face a judge.
That the pages are no longer accessible does not mean the evidence has been destroyed, either. The DMCA requires only that you "block access to" the content, not physically remove it from a server.
The Oatmeal's response to the claim included a list of content infringing his copyright. Funnyjunk is going to want to remove that content to retain its safe harbor from liability for the infringement. It may or may not be a properly worded notice under the DMCA, but a lot of notices UGC hosts get aren't, and they still take down the content -- because the intent of the parties and whether they acted in good faith matters when it's time to face a judge.
That the pages are no longer accessible does not mean the evidence has been destroyed, either. The DMCA requires only that you "block access to" the content, not physically remove it from a server.