If she has willingly executed the stipulation and her affidavit(s) consenting to the divorce then it would be difficult for her to challenge issues of the marriage at a later date. However, it is not unheard of for a party to reopen a case even after a settlement agreement has been executed. The best protection, as a general rule, would be to ensure that she executes the agreement under the guidance and advice of her own counsel - this way she cannot later claim that she had no idea what she was agreeing to etc.
Please note that this general response to your inquiry does not establish an attorney-client relationship.You should consult with a competent attorney for advice regarding your particular situation.
Your lawyer should be giving you advice on this - and it will depend upon where you are in the process.
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She can request to withdraw her consent and interpose an answer. She can also wait until after the judgment is entered and move to reopen the case. It would be best if she had a lawyer represent her, exchange financial discovery and then reach a settlement. In the later case she would face a stiff burden to overcome.
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Your wife can withdraw however, since the stipulation agreement is already signed you have all the issues decided. You could file for divorce if your wife withdraws and just use the stipulation to finish it. Speak to your attorney about what is going on.
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This advice is not meant to create an attorney-client relationship and is a general anwer to the question posed.
If you lawyer has not already done it, you should counterclaim for divorce. This will prevent her from discontinuing the action because the court would just go forward and grant you the divorce instead. I agree that once she signed the stipulation it should control the terms of the divorce, but the fact that she was not represented by an attorney could give the court more leeway to throw out the stipulation.