To my understanding in one path you get the lie and in the other you get the truth. So although it is ambiguous we can make an educated guess based on Chloes motivations and behaviors.
In the ending where the real father lives, Chloe just wants the MC to go away as he has served his purpose. So she tells him that the DNA didn't match but - this is important - we only have her word to go by and it is unlikely because she said it was a rush job using the blood on the clothing. This is less likely to have happened than the test that the real dad ordered. It sounds like bullshit to me.
In the open-ended story where the real father died, Chloe has less incentive to lie (although lets be honest that doesn't mean she has no reason) as his being related to the real dad isn't really a factor in his usefulness to her. She also shows him real test results (or at least a paper with fake ones) instead of just telling him like in the ending. This lends more credence to this being the truth.
Now this could continue to be an ongoing issue but as the VN continues the MCs belief that the real dad is his brother is going to be important. Not to say that Chloe isn't lying to him here and telling the truth in the ending (she has already demonstrated she has the resources to get fake documents) but to my mind Occam's razor slices toward her telling the truth in the continuing story. Besides, it is just a better story that way.