There were some changes in the product, you are right:http://www.veeam.com/files/release_note ... _5.0.3.pdf
Increased Correlation Interval for VMtools Monitor Correlatiased from 600 s to 1200 s
Fixes to reports
Fix to Microsoft Windows 2008 R2 support for VEM
Fix to rawTopology.xml
Fix to Hardware Monitoring in vSphere using vCenter API connection issue
You will also have to uninstall Management Center and Management Center UI to get fully supported solution configuration. This is for your convenience, and I understand it may take you extra 20 minutes to accomplish, but anyway. You wouldn't need to back up anything, but you should take down the accounts in 'nworks Management Center accounts' local group on nMC box, for convenience, as the group would be removed after nMC re-install.
Have a great day,