Should I pay my balance while waiting for 1040x? Will the IRS refund it after the 1040x is filed?

I messed up reporting my scholarship on my 2019 tax return so the "wheres my refund?" says I owe 400 dollars when I should get a tax return. I filed my 1040x in August to amend this. Since it is taking so long to process 1040x, I keep having to call to get payment extensions because they keep sending me notices that I owe the money when I don't. 

 

If I don't keep calling about payment extensions, will they do anything like send it to collections? Should I just pay and then have them refund it once the 1040x is processed? Or should I just keep calling about payment extensions?