It depends on what types of payments you made through EFTPS. If you made individual tax payments, such as estimated tax payments, then it will affect your federal tax return.
For example, if you said you made $4,000 in estimated tax payments and the IRS only has a record of $3,000 then they will reduce your refund by $1,000. If you paid your 2019 balance due through EFTPS and they have no record, they may adjust your refund.
You can call the IRS. Sometimes they put payments into the wrong account or the wrong tax year. Call 1-800-829-1040. Be aware. The phone lines are backed up. The IRS opens at 7 a.m. local time in every time zone. The earlier you call, the better your chance of speaking with someone.
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