Hi ,
Here are some important notes to avoid such issues in the future-1.http://wiki.scn.sap.com/wiki/display/BOBJ/BI+4.0+-+Updating+to+SP04+or+Higher+-+Best+Practices%2C+Known+Issues+and+Possible+Solutions
2. Make sure following best practices are followed before update/installation-
KBA 1952120 - SAP Business Objects (XI 3.1 and BI 4.0) Installation pre-requisites & best practices
Hope this helps.
Regards,
Rukaiya