Below is what someone posted on the same question I posted on IRAhelp.com. What I am wondering is if they would wave the fees through a 5329 since I am trying to get it straightened out "in good faith" since they didn't notice our AGI was over the limit and see the Roth contributions. Luckily, she was only putting $1200/yr in it. Our taxes are done by an accountant down the street. He never asked if we made IRA contributions, and we didn't know we needed to tell him. If he had asked, we could have caught this a long time ago and vice versa. He hasn't been any help on trying to get this fixed. Doesn't seem knowledgeable on the subject although he has done taxes for years, and kept saying the custodian should take care of it all. They say they can only do what I tell them, and that he needs to tell me what needs to be done with previous years. They cannot give tax advice on passed years. Round and round I go. Needless to say, I am done with him after this. (IRAhelp.com answer below)
You are correct regarding recharacterizing her 2015 Roth contribution as a non deductible TIRA contribution, and you can then convert it back to the Roth. Or if the contribution has a significant loss you could request a return of the excess contribution and then make a new non deductible TIRA contribution in the full amount of 5500.
For the prior years, the exact amount of all her contributions should be distributed. This will not be taxable since they are Roth contributions, and any earnings get to remain in the Roth. The main problem is the 6% excise tax for each year which would be reported on a 1040X and 5329 starting with the oldes year. This could be expensive since the prior year excess carries over to the next year. Using an artibrary 5000 for 2010, this would start at 5000, go to 10,000 for 2011, 15,000 for 2012, 20,000 for 2013, 25,000 for 2014 and another 25,000 for 2015. Total of 100,000 @ 6% is 6,000. In addition, the IRS could bill late interest for late payment of the 2010-2014 excise taxes. There is no statute of limitations for excess contributions either, but it would have been nice had the IRS or any tax software program used to complete your return flagged this early on to eliminate this accumulated total.
Since the excise tax accrues on Jan 1, there is no rush to remove her balance before December so might as well let it generate some more Roth earnings for several months before taking out the distribution. But the 1040 X forms should and can be filed earlier to eliminate more possible interest charges. The distribution will be reported on an 8606 for 2016, but unless she has taken withdrawals already, there will be no tax due on the actual distributions.