Google replacing subpages in index with home page?

[ownlocal]

Hi! I run a backlink building company. Recently, we had a customer who had us build targeted backlinks to certain subpages on his site. Then something really bizarre happened...all of a sudden, their subpages that were indexed in Google (the ones we were building links to) disappeared from the index, to be replaced with their home page. They haven't lost their rank, per se--it's just now their home page instead of their subpages.

At this point, we are tracking literally thousands of keywords for our link building customers, and we've never run into this issue before. Have you ever run into it? If so, what's the best way to handle it from an SEO company perspective?

They have a sitemap.xml and their GWT account reports no crawl errors, so it doesn't seem to be a site issue.

[SteveOllington]

What tracking software are you using, and have you checked any of them manually?

[ownlocal]

We built our own rank tracking system (actually getting ready to release this as a separate product within the next couple weeks.) I have checked manually with a non-logged-in Google search and our rank tracker is accurate.

[SteveOllington]

Yeah that's pretty odd then. I assumed it was your rank trackers since we had a similar issue once with ours and it was just an option un-ticked. I have been looking at some of our clients sites rankings today and we're not having the same thing, plus I would assume that it's not something happening to many people, such a change would mean all forums, blogs, etc... with be filled with people asking the same question and wondering what's going on. If that's the case, it means it's just this particular site.

What browser did you use to check manually? It's just that with Chrome it doesn't matter if you're logged in or not, it will still give you some level of personalized results some of the time (which is stupid I know), and to make matters worse, I found FF to be returning completely different results to both Chrome and IE for a few searches yesterday. Maybe it would be worth checking in a couple of different browsers. If it's still the same then I hate to say it but you've got two options... 1) Wait it out for a couple of days in case it's just one of those weird things that do seem to happen, and/or... 2) Start thinking about what changes were made with the site recently to have caused it. I doubt that's at all helpful as I'm sure you already thought of that but like you said, it is bizarre... bizarre Google stuff seems to be happening a lot lately!

Have you got points left to ask in private Q&A? That's probably your best bet since then you'll get one of the SEOmoz staff answering and if they don't know, no-one will.