Normally you should be able to set WHS to suppress these messages from the WHS console, Health Tab.
If that doesn't work you can try:
1. Log on to the WHS desktop (remote desktop is fine)
2. Start, Run, type regedit, Hit Enter
3. Find the key HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows Home Server\Notification\1.0\Sources
4. Below that key you should find a clienthealth subkey with subkeys referring to the error message from the removed computer
5. Delete the subkeys and the whs.clienthealth key for that machine
6. Also check the key HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows Home Server\Notification\1.0\Suppression
7. If you find any keys there referreing to the removed machine delete these also
8. Log off from WHS desktop
9. You may need to reset the console from a client or reboot to the server.