R9ronaldo,
If your Certificate is lost,then you can not get another one from WAEC as you have been told.I don't know what you want to use it for..i.e DV or otherwise.
Do you have the photocopy of it?if yes, you can authenticate the photocopy to either process your admission or Dv or...You will have to send the photocopy,your passport photograph to WAEC and ask WAEC to send the transcript to School or Embassy directly.
You will be required to pay some fee though for postage and so on...
I hope this helps