These situations can be very challenging. My school is highly transient and we often get students in the middle of a quarter. The collaborative, project-based nature of this curriculum makes it very challenging to develop lessons for students who miss weeks of instruction.
This student missed a lot of the norm setting, development of the classroom culture and the expectation leveling for the course. I would focus on making sure they felt welcomed and fully integrated into the class moving forward. One of the great features of this curriculum is the equity focus that allows students to access the content from different starting points. Then, I think it will be most helpful to work with the student, parent/guardian and counselor to develop a plan for how to get the content from the early lessons. I'm sure this is an issue for all of their classes. The content can be 'made up' through the videos, use of "Blown to Bits" and being even more deliberate when connecting lessons and spiraling the content. For grading, it really depends on what guidance your district provides. Are all assignments expected to be completed? Can you excuse some or use an alternate assessments? Are you able to give incompletes or a no grade?
Hope that helped,