How did you "file" that second W-2? The only way it could be done correctly was if you prepared an amended return and printed, signed and mailed it.
The only way to file an amended tax return is to prepare a 1040X and print, sign. and mail it. If you did something else, like try to e-file a change, it went no place.
You can amend a tax return after it has been fully processed and you have received your refund. You must work from your return exactly as it was when you first filed it. Follow the TT instructions to amend a tax return:
https://ttlc.intuit.com/questions/3061514-how-do-i-amend-a-2016-return-in-turbotax
Wait about 3 weeks and you can check the status of your amended return:
https://www.irs.gov/Filing/Individuals/Amended-Returns-(Form-1040-X)/Wheres-My-Amended-Return-1
It will take about 3-4 months for the IRS to process an amended return.