I would be careful in making any determinations based on that alone. Google's index is in major flux right now and I'd be willing to bet that those sites that have added more links to deeper content would have been fine even if they didn't add them. If the content was indexed before, it's there in the database. Google is doing all sorts of shuffling right now and it really pains me to see many chasing that damn algo on a daily basis.
Get away now! Do something more productive. You have absolutely no control over the outcome unless you've really messed something up technically and/or you've been involved in something that presented a level of risk to begin with.