What is the procedure for when you have a group of students and several of them miss the baseline assessment? What about students who leave halfway through and don't come back?

For online students, score the assessments that you can and plan the lesson sequence from those assessments for the group. Make a note on the tracker about which students missed the baseline. If the opportunity arises and you find a session where only the students who missed the assessment are present, you can administer it at that time just to get another data point, but it's okay to just plan the lesson sequence based on the students who were present.