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I have had some P2V's as well and when I update them the historical data does indeed disappear. Un-managing the physical node and recreating a new one would work. You should also be able to generate a report with all the historical information so that it is not lost once you update the system.
When I decommission a system I un-manage it and rename the node to include the status and date of decommission. Example: SYSTEMNAME --> SYSTEMNAME Decommissioned 1/8/2012 (un-managed)