|When you left the old hard disk in the machine it wasn't so bad that Windows installed its system files on that disk even though the operating system was installed on the SATA drive. You were actually booting of the old hard disk.|
You can either put the old hard disk back in with the same configuration as before or reinstall the operating system with only the SATA drive in place.
For future reference when a computer stops working the very last thing you thing of doing is updating the BIOS. A computer that was previously working never stops working because there is something wrong with the BIOS. BIOS hardly ever go wrong, ever.