If this issue is related to one user it’s most likely a user issue or someone has the users credentials. They don’t disappear unless the teacher removes the student from the class or the student removes them selves from the class. We had a case like this, the student just didn’t want to do his classwork so he kept telling IT to “fix it”. Come to find out the student told another student what they were doing, thus told the teacher… Suddenly it fixed it self…
This should be a teachable moment for the teaching staff, students should be taught the responsibility of keeping their data safe.
Admins, can enable auto log off when lid is closed if need be but otherwise a third party add on to disable this feature in google classroom would be required but that means more money.
The only other thing I can think of is if you have another system let’s say a SIS system that is “syncing” with google and someone removes the user from a class schedule with in that System it could also remove the student from the class.
Those are my two cents.