I would start by asking the question why did she file MFS, and what else will change by amending to MFJ? If there was a good reason for filing MFS, that should be considered.
For example, one reason to file MFS is if you know your spouse is cheating on their business taxes. Filing MFJ makes the spouse equally liable for all errors, omissions and problems with the joint return, which you might not want to do.
On the other hand, maybe filling MFS was just a misunderstanding. Filing MFJ is always allowed if both spouses agree, even if one spouse doesn't work or has much lower income, and MFJ almost always results in less tax owed or a larger refund.
Assuming she does amend to MFJ, that would correct the issue. (Amending from MFS to MFJ is always allowed, but amending from MFJ to MFS is not allowed after the filing deadline.)
If she does not amend, we are assuming she did not include a form 5329 to report the excess and calculate the penalties, so she would have to amend those prior returns as amended MFS returns to report the excess and pay the penalties. The IRS will also probably assess interest since the tax is being paid late.
