I found this over at Avforums, so credit goess to Markee over there.
As has been stated on various posts, there HAS been a new version of 3.56 released to fix the replace HDD problem. If you are being blocked from replacing your hard drive, this is what you need to do.
Firstly, you cannot just download the new version 3.56 and install it after putting in your new HDD, it wont work! You WILL get the data corrupt error.
Secondly, you will need the old HDD you removed from your PS3, still intact with your PS3 files on it - if you have formatted it for use elsewhere, sorry, you are buggered until Sony release a proper fix!
1. Put your old HDD back in your PS3.
2. Switch on and login to your user profile.
3. Go to system settings and install system update (I just used the version I had copied to my USB stick, this effectively updates the firmware from 3.56 to 3.56 fixed).
4. Once the update has been installed, and your PS3 has restarted, power down and remove the old hard drive.
5. Install your new drive, and when the PS3 checks the update file on the USB stick VOILA! it works!
You can now follow the process on page 1 of the how to upgrade your HDD thread.
Oh yeah, not impressed with Sony for their lack of care for customers, lack of communication and tardiness in fixing this problem!