There are two issues you raise here. First of all, Married couples can always file separately for whatever reason whether living separate or apart so the filing of separate returns does not ratify the agreement that you had drafted but never signed. That agreement probably stated that you guys had the right to file separately or jointly as long as you remained married. The second issue however about whether she can get a share of what you accumulated after the agreement is more important. Under New York Law, any property acquired during the marriage is marital property subject to equitable distribution regardless of what name it is in until the filing of a divorce action or filing of a separation agreement. So if the separation agreement was never filed, theoretically each of you are entitled to any property te other has accumulated until a divorce is filed or the agreement signed and filed. This does not necessarily mean that she will be entitled but she certainly has a legitimate right to seek it and it will depend on a number of factors as to whether she will in fact get any part of it. You should certainly seek the advice of a matrimonial attorney in the County in which you reside to discuss your options and how to proceed from here.