Incase anyone wants to know how I eventually did it, please note that I formatted everything as I had nothing to lose!
First, download the update tool from the buffalo website and extract it out somewhere.
Then, change the linkstation_version.txt file and increase the version numbers by ten.
I had to change the lines "VERSION=1.35-1.39" and "BOOT=1.19" to "VERSION=1.45-1.49" and "BOOT=1.29".
Now change the .ini file and add the following to the bottom of the file:
VersionCheck = 0
Debug = 1
Now run the update tool, and click on the logo in the top left hand corner and then the debug option.
On the next screen, select all of the tickboxes in the top half and select okay.
Now you can update the TS Pro, just follow any instructions on screen.