data warehouse contains duplicate data from across multiple repositories, help?!

we run multiple repositories (ccms), and collect all the data into a common warehouse, using Rational Insight (and its etl data movement jobs).

now all the workitems are in one big common database.. (we know we have duplicate workitem IDs)

for business reporting purposes we need to report on the iteration a workitem is in, but when we look for a specific iteration name from its ID, we are getting multiple results.  it appears the calculation of the iteration uuid is good for one server, but may cause duplicates across servers.  help..