Loss of rankings due to hack. No manual penalty. Please advise.

[digitalimpulse]

I have a client who's site was hacked.  The hack added a fake directory to the site, and generated thousands of links to a page that no longer exists.

We fixed the hack and the site is fully protected.  We disavowed all the malicious/fake links, but the rankings fell off a cliff (they lost top 50 Google rankings for most of their targeted terms).

There is no manual penalty set, but it has been 6 weeks and their rankings have not returned.  In webmaster tools, their priority #1 "Not found" page is the fake page that no longer exists.

Is there anything else we can do? We are out of answers and the rankings haven't even come back at all. Any advise would be helpful. Thanks!

[StreamlineMetrics]

Any chance you can share the URL here or via PM? Also, for the fake page showing up in GWT as the top priority, did you click on the link to see more details? Such as where it is being linked from? That might provide some insights as to why Googlebot is still trying to access that page.

[digitalimpulse]

Thanks for your reply.  Sent you a message.

[MarieHaynes]

Are you absolutely sure there isn't something else going on?  Usually Google is pretty good at picking up this type of thing and just discounting the links.  Plus, if the links were generated to pages that didn't exist then they wouldn't be passing any signals (i.e. penalty) to the site.  In fact, removing pages is a way to remove links.  (See http://searchenginewatch.com/article/2296653/Removing-Unnatural-Links-by-Removing-Pages-on-Your-Website)

You mentioned it happened about 6 weeks ago...I'm not sure if it fits, but 4 weeks ago there was a very large Panda update that upset a lot of site's rankings.  Any chance the drop happened around May 20?

Have you checked WMT and sucuri.net for signs of malware?  Often when pages get injected like that it comes along with malware.

I'd also look for things like accidental noindexing or blocking pages with robots.txt.  I had three sites this week consult with me because they thought they had penalties and two had lost their analytics code and the other had accidentally noindexed the majority of their site.

If the ranking drop is indeed due to the bad links then you really should recover now that they've all been disavowed.  But I'm guessing there's something else going on.