At this time, you cannot directly edit the names of reference data layers, or any layers that you have previously uploaded or saved as filtered selections. You can, however, effectively create a copy of a layer and give it a new name.
To do so, use the Filter controls to select all of a layer's features, then save the selection as a new layer with a new name. You can select all features in your project area by adding a join filter to the Project Area layer as shown in the example below. (If you created a project with a context area, you could instead add a join filter to the Context Area layer.) Once you click Save as, you'll be prompted to enter a name for the new layer. You may then choose to remove or delete the original layer, if no longer needed.
Using the Filter controls to select all features and save as a new layer with a custom name