Ok after more searching I found a thread relating to this that recommended running clean all on my HDD.
Not really the best option to wipe 300gig of information from a drive which is partitioned, and the process described here
didn't seem to give any other option but wiping the whole drive.
Instead I have opted to format C:, which would leave all my information available still on D: and E: partitions.
Is there any reason this will not work?