I came across an interesting post on the FlexRaid forum that provides a step by step guide of how he migrated from the original version of Windows Home Server to the 2011 version of WHS and added FlexRaid to provide parity protection to his data.
The introduction to the post indicates that he had to copy his data over to the new NAS configuration:
I just recently went from WHS v1 to WHS 2011. I had around 12TB of data to move, 16TB worth of space. I know you can technically just 'inherit' data into a FlexRAID setup, but that gets kind of confusing because of WHS v1 file structure, duplication, etc. I just spent the extra few days copying files and starting with a fresh FlexRAID pool.
Source: FlexRaid Forum
Even with having to copy the data over, the overall process as provided in the post seems quite doable without much trouble. I really enjoy this sort of walk through that will simplify setting up a server.
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