You may have noticed on your board that your Done column automatically archives issues off of the board after 30 days of inactivity.
If you're using multiple done columns in Waffle (read more here), it works a bit differently.
Only the column in the "Closed" section without a column label will auto-archive. All other columns in the section will not do this.
The example below, we have 2 columns in the "Closed" section: Done and Shipped.
Because the Done column does NOT have a column label, any issues that remain in this column for over 30 days will automatically be archived and removed off of the board.