It means you have to pay more. Did you pay the $3,000 bill? Did you start the Amended return before you entered any new or changed info? Did you have a refund on the original return? You might have to pay some of the refund back plus the extra tax. What did you have to amend for?
The amended return will only be the difference you get back or need to pay. You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 21 should be your additional refund. If you paid on your original return it will be on line 16 (but don't include any penalty on 1040 line 38). If there is an amount owed with the amendment, it will be on line 20.
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