Firstly, she must contact the solicitor who deal with the appeal. It is their job to act on her behalf and inform her of the appropriate position following determination on appeal and how this affects her leave to remain. This is what she paid them for and if she has not heard from her solicitor then she should press them for a response now.
I will answer on the assumption that she does not have leave to remain and is, in effect, an overstayer from the date that he previous visa application was rejected.
The overstay affects most forms of visa application but by virtue of Immigration Rule 320 the UKBA are not permitted to reject an application for spouses visa on the basis of the ovestay alone. Provided her application for a spouses visa on the basis of her marriage to your son does not contain any other defects then the UKBA would grant her a spouses visa.
The difficulty is that if she does not have valid leave to remain then the UKBA will ask that she return home and make the applicaiton from there. She would only be able to make the appliaction in the UK in the most exceptional circumstances, this is usually where to remove her would severly affect another's person's health (eg. a husband in poor health or child that she must care for). This does not appear to be the case here and therefore the UKBA would ask her to return home and submit the application to the Embassy there.
This is probably what she is going to have to do. In order to get her back here as quickly as possible I would advise that you see a local immigration solicitor and ask that they prepare her application and supporting documents before she leaves. She can then submit it to the Embassy as soon as she arrives. They will reach a determination on it within 6-8 weeks usually.
I can advise you of the eligibility criteria for a spouses visa if you wish. Please let me know if you want me to.
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