You can mark an email as Done with either method:
- Using the Bottom Bar Actions in Mail View.
- Using Swipe Options in List View.
A Done email appears in the Done column of the Later Board, alongside the columns where Reply Later mail waits. The message stays in your inbox as well: Done marks it handled and read rather than moving it anywhere, so nothing is deleted or hidden.
Note that Done is not one of the mail-list Filters; those are All, Unread and Starred.