Reformat the second hard drive - the one with the failed operating system. Then, follow these steps to stop it from asking you to choose an OS:
Run WindowsXP off of your master hdd
Go to the control panel
Go to System Properties
Go to the Advanced tab
Click on the Settings button next to Startup and Recovery
Click "edit" to edit the startup options file manually
Delete the extraneous information about the second operating system. For example, this is what my boot.ini file looks like, configured for only Windows XP Pro:
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows XP Professional" /fastdetect
cscgal
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DMR
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