If the Phatbox was successfully hacked, as it appears it was, there is no need to run the hack again -- unless the hack was unsuccessful, and it only worked as a fluke with the non-orginal DMS, which is extremely unlikely.
You wrote that you used version 2.10 of the Phathack tools. 2.12 is the latest version, and that's what you should use.
You also wrote that the PB originally had firmware version 5.01. The last VW firmware version is 7.02. After you ran the hack, which version of the firmware did you load onto the new DMS? Did you ever flash the PB with 7.02 firmware?
These points aside, usually when a DMS goes from working to not working, the drive is failing. It's even possible that the 40GB drive is failing too, by coincidence. I've had two DMS drives fail, and it seems the PB is more sensitive to drive faults. Whatever else you might need to do, I suggest you run a full disk check (with surface scan) on whichever drive you intend to use as a DMS.