One other possible cause could be a faulty enrolment plugin (or just badly configured). E.g. if the students are removed from the course (maybe a DB query is failing some of the time) and re-added they will lose all their grades and submission data.
Different enrolment plugins have different settings that affect how this works e.g. external database has "External unenrol action
enrol_database" which should probably be set to "Disable course enrolment" for the safest configuration.
This discussion has been locked because a year has elapsed since the last post. Please start a new discussion topic.