Before this Flash update was available, the only way to upgrade a 2009 machine to a Westmere (6-core) was to do a Motherboard swap to a 2010 board (backplane board), which can be done and works. I have a friend who did this.
The reason for this was that that the firmware that supports the B1 stepping is only on the 2010 boards.
The Flash tool now available will change your 2009 board (which by default only supports D0 stepping/Nehalem) to support the Westmere B1 stepping which is used by the 6-core processors.
So, yes, by applying the flash upgrade (flashes the firmware to your backplane board), and then dropping in your Westmere 6-core W3680 or W3690 processor, and of course carefully putting on your heatsink with thermal paste, you should have a working 6-core Westmere machine.