Hi and welcome to Just Answer!Will irs issue a refund to me for the amount they owe me for 2012 minus the amount they claim I owe them for the other years, or will they wait until they render an opinion on the penalties, then issue the refund? If you are due a refund - that refund will be issued. If you are under collection for previous years or if you stated that refund must be applied to other tax liability - the refund will be issued - but will be offset by your tax debt. In case your refund will be offset - all tax debt will be considered - actual tax liability, penalties, and interest charges.About how long does this take? Since the 2011 amended return was mailed in the same day I efiled 2012, obviously it would not include that correction.Processing time for 2012 efiled tax return might be about 2-3 weeks.Amended tax returns are processed longer - generally 4-8 weeks.
In some situations processing time might be longer.It is hard to predict the exact processing time.You may verify the status of your amended tax return on this page - http://www.irs.gov/Filing/Individuals/Amended-Returns-(Form-1040-X)/Wheres-My-Amended-Return-1