|Were the 2 drives running in some RAID setting? |
If you don't want to use any RAID then you can install non matching drives. You don't necessarily need NCQ either. The concept is good but probably not much difference in real world performance.
Your system may have originally been set to run RAID 1 mirroring. If the one drive is still working OK then that is the likely setup. Either that, or they were simply independent and the OS just happened to be installed on the working drive.
RAID 1 writes the same exact data to both hard drives. Therefore, both must be the same size or the larger one will not utilize the excess capacity. Some controllers may not like unmatched hard drives either.
Do you need mirroring? You could perform regular backups to get the same results. What is the computer used for?