Hundreds of Thousand Spammy Backlinks Overnight

[JDLitchfield]

Hello,
I have a client who unfortunately got breached (not sure how) and as a result 6 HTML files promoting gucci bags and Louis Vuitton bags were put in the root.
I found the files within a week of them being put there but what I didn't realise (and only found yesterday when looking at the backlink profile) was that there are literally hundreds if not thousands of spammy domains pointing at these files.

Some of the sites 404 but some are posts on other bloggers sites who auto accept comments and they total 10,000 links so impossible to remove.

Question is:

1. Will Google understand what has happened and ignore these links (especially because the pages don't exist on the server?)

2. Should I use the Disavow tool to block these 1000 odd domains (can it do any harm?) and more links are being found every day so do I just keep doing it?

3. Is there another way to explain to Google what has happened?

Your help would be greatly appreciated.

Thanks
James

[MarieHaynes]

Wanted to add one more thing.  If it's possible, you may want to use the url removal tool to remove these new nasty pages from the Google index.

[MarieHaynes]

If you remove these pages so that they serve a 404 or 410 error then it will essentially remove the links and Google will pay no attention to them.  More info: http://searchenginewatch.com/article/2296653/Removing-Unnatural-Links-by-Removing-Pages-on-Your-Website

You could definitely disavow these links and it would not harm your site to do so.  Do it at the domain level, not the url.  With that being said, if all of the links point at pages that are now removed then there's no need to do so.

Google is usually pretty good at understanding what is going on.  This type of link really shouldn't cause you harm.  With that being said, I would run the site through sucuri.net to look for malware as often hacked sites will be hosting malware.  If Google determines that there is malware on the site then it will try not to send users your way and you'll get a malware warning in WMT.