Recently I had to query a list in a meeting workspace, but I got an empty resultset for every meeting except the first one. Seems that tools like the U2U CAML Query Builder and SharePoint Manager 2007 were only able to query the items of the first meeting. Time to start googling and after some time I found a post of Sanket Shah describing the same problem I had. There is one property, ‘query.MeetingInstanceId’, you have to set on the query, if you want to get items out of a list other than those of the first meeting. It won’t work if you add the Instance ID column to your CAML query.
Code example (list is an SPList):
Dim query As SPQuery = New SPQuery()
query.Query = YourCAMLQuery
query.MeetingInstanceId = instanceID
Dim results As SPListItemCollection = list.GetItems(query)