IRS questioned 2017 refund, which was applied to 2018 est. tax. 10/15/19 they sent a check. Now my 2018 is wrong. Do I need to file a 1040-X because of their error?

Thank you Critter.

The more detailed background.  They question a portion of my 2017 refund which had been applied to my 2018 estimated tax.  After sending all the documents they wanted I assumed everything was OK.  I finally filed my 2018 taxes Oct 14.  On the 15th I received a check, and a letter stated my 2017 taxes were correct.  Unfortunately, that refund should have been applied to my 2018 estimated tax.  Now the 1040 is incorrect, as the funds should have been applied to estimated tax... I called IRS and was on hold for 135minutes. If I try to file a amended 2018 with Turbo, it says I own money, when in reality they own me another refund (I over paid just in case they didn't credit me)  ONly way I see to fix now is to file a amended return for 2017 and 2018...or ignore, as the final amount they owe me is the same.   Sorry for the length!