What do you mean by filed two separate w-2’s? All your W-2 forms and all your other income( if you have any) should be reported on the same return. You can't file more than one return. If you tried to file another return to report a second w-2, that return will be rejected.
You need to amend your first return and include the other W-2.
Follow the steps in this link to amend your return.
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