You will need to review your separation agreement in order to determine the effect of reconciliation on the terms of the agreement. Typically, separation agreements will have the following provision (or one that is substantively similar) included:
"This Agreement shall not be invalidated or otherwise affected by reconciliation between the parties hereto, or resumption of marital relations between them, unless said reconciliation or said resumption be documented in a written statement executed and acknowledged by the parties with respect to said reconciliation and/or resumption and, in addition, setting forth that they are canceling this Agreement. "
If you are certain that you and your spouse have reconciled, you will need to properly execute a new agreement expressly voiding the terms outlined in your Separation Agreement. Please consult with an attorney prior to taking any action in connection with your previously executed Separation Agreement.
You and your spouse can sign and file a Stipulation (in front of a notary with the acknowledgement language) stating your intent to terminate the legal separation entered into on....(whatever date it was signed). You should speak wiht a local family law attorney to help you.
If you are asking how to go about nullifying your seperation agreement, then you have to see what is required by the agreement. If you want to leave the agreement in force then all you have to do is resume living together but know that if there are difficulties in the future the agreement still holds. You should discuss your options and what is in your best interest with an attorney before doing anything.
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This advice is not meant to create an attorney-client relationship and is a general anwer to the question posed.