We had this problem also..Cognos sugestion was to upgrade the cubes using their cube swap utility
If you want to rebuild the PowerCubes you can use the cubeswap utility.
As stated on the Admin and Security Guide:
Update a PowerCube Connection
If a PowerCube has been rebuilt, you can update the connection information without affecting
current users. To do this, you must first update the connection information to the rebuilt
PowerCube, and then refresh the report servers to use the rebuilt PowerCube for new connections.
The updated PowerCube will be used for all new sessions referencing that data source. Any user
that has an active session against the data source may have to re-open their session. Old
PowerCubes can be removed only after all sessions using that PowerCube have ended.
When you rebuild the cube, we recommend that you use a new name for the PowerCube, such as
including the current date in the new name. You can then store the rebuilt PowerCube in the same
location as the old PowerCube. For convenience, Cognos provides the sample script cubeswap.bat
or cubeswap.sh that is located in the c8_location/webapps/utilities/cubeSwap directory. You can
get more information about the script syntax by running the script without any parameters.
Tip: You can automate this task using the Cognos 8 SDK to hot swap PowerCubes. For more
information, see the SDK Developer Guide.
Steps
1. On the portal toolbar, click Tools, Directory.
2. Click the Data Sources tab.
3. Click the data source representing the cube you want to update.
4. Click the set properties button for the connection you want to update.
5. Click the Connection tab.
6. Click the edit button for the connection string.
7. Change the file path and name to point to the rebuilt cube.
Tip: To test whether parameters are correct, click Test. If prompted, type a user ID and
password or select a signon, and then click OK.
8. Click OK, and OK again to return to the data sources page.
9. On the portal toolbar, click Tools, Server Administration.
10. Click the Configure tab.
11. Click the refresh report services connection button.
Any new connections to the PowerCube will use the updated cube.
You can also have a look at KB
http://support.cognos.com/knowledgebase/googlesearch?load_kb_document=1&dr=kbcdr&uniqueid=133222 
