You need to edit your boot.ini file to remove reference to the windows 2000 install you deleted.
Boot.ini controls which OS boots up. Thus by deleting non-existent entries, it will not prompt you for those.
Also by changing the timeout value in the timeout entry line to zero will result in the default always being used without any further prompts.
If you dont like to do this manually then I believe there are admin tools that will allow you to do it.
Here is an example boot.ini of my triple boot system. Note the default is Windows 98SE as defined by the default line.
[boot loader]
timeout=15
default=C:\
[operating systems]
multi(0)disk(0)rdisk(1)partition(1)\WINDOWS="Microsoft Windows XP Professional" /fastdetect
C:\="Microsoft Windows 98se"
C:\man100.lnx="Linux Mandrake 10.0"
To give you an idea on defaults, for different defaults I would replace default line as follows:
default=multi(0)disk(0)rdisk(1)partition(1)\WINDOWS
default=C:\man10.lnx
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