If you are looking at the refund meter - the refund meter during the amendment process only shows the differences from changes you made from your original return. Your original refund will still be paid to you. So, if your original refund was $1000 and now after changes it says you owe $100, that means you have to send back $100 from the original $1000 refund, not that your entire refund has been lost and now you owe $100.
Please review the article below and make sure you followed the amendment steps properly. You will need to print and mail both your federal and state amendments. You will need to pay whatever amount you owe, but you should wait until you receive your original refund before you mail the documents and payment.
https://ttlc.intuit.com/replies/3288565
Also, when you add a W2, it is common to wind up owing money back. I have included an article below about this scenario.
https://ttlc.intuit.com/replies/3798403