The COVID-19 pandemic has led to school closure and home confinement globally. There is an urgent call for researchers to understand the impacts of the pandemic on students' well-being. Since January 2020, school students in Hong Kong have experienced an extended period of over 100 days of school closure, a short period of school reopening when the pandemic spread subsided, followed by a government directive for earlier than scheduled summer vacation due to the third spike in COVID-19 infections. This paper reports on a study that investigates how students’ physical, mental, social, digital, and academic well-being may be affected during the aforementioned three phases in schooling arrangement, as well as the factors that may protect or aggravate students against various potential challenges to their well-being during the pandemic. Using a combination of convenient, purposeful and snowball sampling, 22 secondary school students, 20 parents, and 3 teachers participated in this three-phase study from April to July 2020. We extended the Day Reconstruction Method (DRM), which is an established method to facilitate participants' recall of the episodic event-sequence, by leveraging mobile apps and wearable devices to semiautomate the process. The DRM data is Supplemented by in-depth interviews with students, parents, and teachers. Analysis results reveal a number of impacts brought by home-confinement, the positive benefits of school resumption, and the emotional value of social connections during the pandemic. These findings have implications for teaching and learning under the changing contexts imposed by societal events