After you file

First, you don't file W-2 forms; you file a tax return using information contained on your W-2 forms.  
It sounds like what you did was to file a tax return when you received a W-2 form, using TTax On-Line.   Then, a few weeks later when you received a 2nd W-2 form you filed a second tax return --using the same TTax On-Line account.

Since the TTax On_Line product can only be used to file one (and only 1 return), when you entered the information from the second W-2 you totally and permanently erased all information from your previously filed tax return.  

When you received the 2nd W-2 --after having already filed your tax return-- your should have filed an amended tax return (Form 1040-X) with the added information.  The amended Form 1040-X must be PRINTED and MAILED.