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After you file
@tonybeo wrote:
Thanks. But if I pay, am I agreeing to their findings and then am I no longer eligible to dispute their findings?
No. You are not agreeing to their findings. Not for a typical automated math or data entry error. Not at all. In fact you can even just pay online at https://www.irs.gov/payments
[Edit, you could just mark it as an payment on 1040 or even 1040-ES. It will basically be added to your account and if its the right amount it will stop their automated request for more payment.] As @Mike9241 says if you receive something other than a simple notice of math/data error that is a different matter. A Statutory Notice of Deficiency or a CP540 Notice of Intent to Levy (seize) are very different and should be dealt with promptly, ideally with professional help.]
You generally have 3 years from your filing date or 2 years from a payment or tax assessment (which is later) to file a request for a refund. It does not need to be resolved by then but you need to have started the process. (Amended return, letter, etc.)
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