Try reading Technet article Q228004:
http://support.microsoft.com/default.aspx?scid=%2fsearch%2fviewDoc.aspx%3fdocID%3dKC.Q228004
(please remove any spaces)
Perhaps in adding the new drive, Windows got confused and labeled the CDROM drive as the "active" drive letter. It is the active partition that Windows tries to boot from. And if it tries to boot from the CDROM and the Windows files (including NTLDR, NTDETECT.COM and BOOT.INI) are not there, your system will not boot.
You can also try making a Windows 2000 boot disk. Just copy NTLDR, NTDETECT.COM and BOOT.INI from another Windows 2000 machine (or extract them from the CD), and make sure the ARC pathing in BOOT.INI matches up with the pathing on your Advanced Server (the typicalARC path, where Windows is installed on C:\WINNT, looks like this:
multi(0)disk(0)rdisk(0)partition(1)\WINNT="Microsoft Windows 2000 Server" /fastdetect
Hope this helps.