How can we refresh the data in our 9.02 environment from 8.12, without wiping out new tables, access

We created DV 9.0 by upgrading a copy of DV 8.12, then we applied Update 2 and code current.  Once we were sure it was stable we copied DV 9.0 to create PY 9.0.  Once that was stable we attempted to refresh the data in PY 9.0 before we started User Acceptance Testing.  To refresh PY 9.0, we deleted its data library and replaced it with a copy of our PD 8.12 data library, then ran the upgrade over the data tables.  But the upgrade doesn't take into account Update 2 and code current!

The result is in our PY 9.0 we are missing over 400 new 9.0 tables, multiple access paths, and all table changes that came with Update 2 and code current (we can see them in DV 9.0).  This is preventing our PY 9.0 from functioning - for example, we can't run any program that updates the sales order files. We get an Asynch error, then Fail to Commit.  We've had to cancel UAT.