If Boot.ini is MIA Ntldr will display the advisory message you spotted and automatically boot from the Windows folder in C: (in Win 2k it will boot from C:\Winnt) - this is a default selection in Ntldr. Booting will be successful provided there is an OS installed in C:\Windows or C:\Winnt
The only problems are that in a multi-boot configuration the boot menu will not be displayed and options will not be activated. Replace your Boot.ini file.
See
http://support.microsoft.com/kb/314081 and
http://technet.microsoft.com/en-us/sysinternals/bb963892.aspxGood luck.