The difference has to do with when she lost her phone. "She has lost..." is a current statement of her status. It is still lost. "She had lost..." is a reference back to when she lost her phone. It may or may not still be lost. In using the second choice, there would normally be further comments to explain, such as: "She had lost her phone last week, but has found it now."
Had lost = Past perfect always suggests two past events. She had lost her phone in the hotel lobby on her vacation last week, (event #1), but a nice person found it and turned it in . So she got the phone back (event # 2)
Present perfect - suggests event(s) initiated in the past which is still connecting to the present Ex: Paul has worked for Google since the founding of the company.