It sounds like after you updated the parent project, the directory entry that was previously using that sub-project is now empty. The second screenshot does not show this, but instead shows the subproject common_specific as absent as if it has been unused from the root directory.
Assuming it is an empty directory entry (displayed with a red exclamation mark), this means that the sub-project does not match the criteria for the update properties of the parent project. That could occur if the subproject uses a different release or purpose with respect to the parent, or has an incompatible platform setting with respect to the parent. One way of diagnosing such things is to enable verbose on update members, perform an update on the project (without recurse) and look at the messages in the message view. It would probably be best to use the expected version of the sub-project first, then perform the update members, and then look at the verbose messages to see why that version of sub-project was regarded as an ineligible candidate.
You can find more information at:
http://www-01.ibm.com/support/docview.wss?uid=swg21325696
http://www.youtube.com/watch?v=jcxC_XMtMqU
The second link is a video clip that explains how to use verbose messages from update members to diagnose such issues.
Best regards,
David
