Hi, here's some information regarding restore for Windows 2000.
I am not sure if this is related  but just providing you the information
that might be helpful in PD your issue.

http://www-1.ibm.com/support/docview.wss?uid=swg21164812


Sung Y. Lee

"ADSM: Dist Stor Manager" <ADSM-L AT VM.MARIST DOT EDU> wrote on 11/28/2005
02:38:40 PM:

> I was resinstalling a Windows 2000 server for disaster testing and it
wont
> reboot after reload. I was following the instrutions found in the
> pdf  "Disaster
> Recovery Strategies with TSM"
>
> I successfully restored the C: drive and System object, I then choose to
> reboot and Windows doesnt start and gets the message
>
> Windows 2000 could not start because the following file is missing or
corrupt:
> <windows 2000  root>\system32\ntoskrnl.exe
> Please re-install a copy of the above file.
>
> Has anyone seen this before with a TSM restore, Both client and server
are
> running TSM 5.2.3. Windows server is 2000 with SP4.
>
> I did get a popup before I rebooted stating that some Windows files had
gotten
> replaced and it need the install CD. I figured that I could ignore
> that since I
> was doing a full replace anyway.
>
> Tim Brown
> Systems Specialist
> Central Hudson Gas & Electric
> 284 South Ave
> Poughkeepsie, NY 12601
> Email: tbrown AT cenhud DOT com
> Phone: 845-486-5643
> Fax: 845-486-5921