Probably the problem is in the boot.ini file only...
If you can see the files there, simply edit the boot.ini to point to the correct partition.
See
http://support.microsoft.com/kb/102873 for a description of arc paths and suggested edits you may need to make.
Example - original arc path may read:
multi(0)disk(0)rdisk(0)par
tition(2)\
WINNT="My Server 4.0"
and you simply need to change it to
multi(0)disk(1)rdisk(0)par
tition(2)\
WINNT="My Server 4.0"