In the most recent version of Atom, v1.6, a new Pending Pane Items feature was added that is described here:
There are a few ways that you can make a “pending” item permanent:
- Double-click the tab for the pending item
- Save the file (even if there are no changes)
- Edit the file
You can also disable the feature by going to the Settings View and unchecking “Allow Pending Pane Items” in the Core Settings section.