"why can’t the IRS see the changes and just deduct the difference before depositing our refund?"
The processing of original returns and of amended returns are done by separate areas within the IRS. Thus, for many years, you treated the payment/refund on the original return as separate from that of the amended return.
Because you can amend a return more than once, it is not practical for the IRS to wait to see if you have another amendment coming that they should net your refund/bill against.
2020 has been a difficult year for everyone, especially the IRS who are having to deal with Congress "moving the goalposts" on a daily basis. Each one of these law changes require concomitant changes in the software at the IRS as well as in all sorts of internal processes. Let's look forward to a better 2021.
**Say "Thanks" by clicking the thumb icon in a post
**Mark the post that answers your question by clicking on "Mark as Best Answer"
