Let me correct:  As you get OPT you are can file tax 1040 and you do not worry about 1040NR for that tax period. Just add the new w-2 amount and amend, just couple hundred dollars depending up on the dollar you amount on that new-w-2 form.

How you do:

First, Redo your tax adding all the w-2 forms and print out it, gives the glimpse of your  correct tax filing, and will help you  to compare the reasons for differences and where  the differences are. Did you do it online or the software you bought?

If you have done online, you have to go amend and will guide you through it.

If you do not have complicated tax ( just w-2s) advise to use tax-act.com which is same as turbo tax and cheaper to file ($20 or less for state and federal). Some one may suggest there are free filing software too, year  if you are illegible you may able to file free federal and state.

For your future reference: If you filing tax try to do it manual way and it will make you read the instruction and will give you full idea what part of that form is related to you. Then when you do online, you will know which part to skip and which part you should not be missing and if missed what did you miss and look for it.
Good luck.