For a fix, I dont think you can help your installation... usually when data corruption is large enough that your seeing it in your GUI its pretty deep into your installation.
Having said that, I highly recommend putting such a large install on a partition that is not shared by your operating system. Windows does a terrible job of fragmenting your directories, swapping files and general os nonsense that it only takes a while for something to go corrupt.
On top of putting the installation for SHIII in another partition, if you have the space... make two separate installations of SHIII. Patch both of them up and set one up as an archive which you'll never, ever.. play from. If you get data corruption... just copy and paste the installation over your old one.
Make sure you check your HD for errors and defrag before you do a large install as well. Its prolly not a bad idea to check your registry for errors before you start this whole process wither.
Oh yes, I wanted to add that I have used a method like this for years after experiencing what I felt like was too much data corruption. I ran one game for around 3 years and just recently reinstalled so I could upgrade to GWX3.0.