Time-synchronized state estimation for reconfigurable distribution systems is challenging because of limited real-time observability. A system addresses this challenge by formulating a deep learning (DL)-based approach for topology identification (TI) and unbalanced three-phase distribution system state estimation (DSSE). Two deep neural networks (DNNs) are trained for time-synchronized DNN-based TI and DSSE, respectively, for systems that are incompletely observed by synchrophasor measurement devices (SMDs) in real-time. A data-driven approach for judicious SMD placement to facilitate reliable TI and DSSE is also developed.