In Waffle, the "Done" column empties issues after 30 days of inactivity on the issue.
If you close an issue and then update it (with a comment or label, for example), the 30-day clock resets. Issues closed after this time are always accessible directly from GitHub. If an issue is reopened, all previous attributes will display on the card (size, label, assignee, etc..).
You can view your archived issue in the Metrics section on your board. Read more here: View archived issues