Hi Mary,
Please may I know what upgrade are you performing on the system and could you please provide the error details? I have recently faced this issue during source system connection setup on our BW system.
Please see if the below threads would help you:
http://scn.sap.com/thread/85944
Source system activate/restore
and below check the below SAP note
1492773 - T-Code RSA1 - Entry in inbound table already exists (Message no. E0412)
Regards,
Pradeep