In order to properly answer your question authoritatively, I would have to examine the written Separation Agreement you refer to. Assuming that the information you stated is absolutely correct, your husband should have no recourse to now claim an interest in the houses.
If you are considering completing the process of filing for divorce (it is time you completed the process and get on with your life -being separated and not divorced is the worst of both worlds). Please call may at 212-370-1660 to discuss mediating the divorce which will save you time, money, and a lot of aggravation.
Leonard M. Weiner, Esq./Divorce Solutions