A 1099S was issued to mother and daughter. The daughter lived in home for 4 years. How do I treat mother's 1099S?

You'll need to establish your facts a bit more clearly to determine the appropriate reporting position. 

• If I understand you correctly, the mother and daughter are both on the title, presumably, as joint tenants;
• While you clarified how some of the maintenance costs were paid, there's no mention of how the down payment was funded (and if any portion funded by the mother is to be recovered and how);
• It is interesting also that you mentioned that the mother expects the upgrade and fix-up expenses to be repaid that there's no word about the mortgage payments made in the initial two years; and
• There's no indication how the proceeds from the sale would be allocated between the mother and daughter.

Case laws would generally determine equitable ownership based on who take up the burdens and benefits of ownership, looking beyond whose names are on the title.  The burden of proof is on the taxpayer and this would entail not only documentary evidence (such as loan agreements and quitclaim deeds) but actual facts.

If it is to be argued that the daughter is the sole equity owner, you will need to construe a case based on these factors, which seem to be lacking based on the limited info you have shared, and discern whether there was ever any element of gifts in the equation.  There appears never to have been any formal agreement for the repayment of sums made by the mother in terms of the down payment and mortgage.  Even if there was, the question is whether those terms were enforceable and ever enforced.  Especially with the mother paying for the upgrade and fix-up expenses right before the sale, unless it is contended that what the mother had funded for down payment and mortgage was a gift to start with, it could further reinforce the presumption that these works were carried out at her expense (or fronted by her) to protect her interest and maximize the sales price of the home.