Well firstly, no medium is safe, regardless of external or internal, physical or Logical. Although it is a good idea of keeping your data on an external drive however that can cause issues as well (as it is connected via USB or Firewire ports). Additionally you can save your data on to the DVD discs however they can be scratched. You can also save the information onto the SD cards/USB sticks however that can be damaged too.
In addition to that there could be a security issue as your data is lying around in multiple locations and if disc or external hard drive get lost, you going to loose your information.
As regard to your issue of the corruption I would have taken the hard drive out and put it into another machine as a slave and moved all my data. The physical data does not get damaged upon OS damage.
Another strange thing is, when your computer came with pre-built two partitions how could a recovery disc made 1 single partition unless or otherwise chosen to do so. The Recovery discs are images of the actual computer when sold. So if it was with 2 partitions it should have made 2 partitions as it came new.
Saying that it could have been many things which could have caused a single drive partition.
Although the data can be lost pretty easily in any medium including USB sticks, however, USB sticks are the most verstile and easy to carry mediums. I usually use USB sticks with my everyday used data (either it is documents or music etc).