Nope. Penalties are only refunded by the IRS under extreme circumstances, and your situation isn't anywhere close to extreme. Nobody twisted your arm and held a gun to your head forcing your to file MFS in the first place. Also, chances are fairly good your amendment may come back to bite you. Generally, a married couple can not change their filing status once the filing deadline for that tax year has passed. I'm surprised it went through. But there are situations where it would be excepted. However, I can't think of a single one where the change from MFS to MFJ would be accepted more than 2 years after the original filing. (Not to say that such a situation that would allow it may exist)
