In the AddEdge sub-directory created by the align_epi_anat.py script, you should find an examine_list.log file. That file contains a list of the files to display by the AddEdge script. Here is a way to check if they all exist.

set elist = `cat examine_list.log`
ls -l $elist

If any are missing, you should see an error that says "No such file or directory".

You can run @AddEdge directly in that directory by running something like

@AddEdge epi_ns+orig anat_ns+orig anat_al+orig

Then run @AddEdge again without parameters to see the datasets.

afni -niml -yesplugouts &
@AddEdge

The AddEdge support for the align_epi_anat.py script and @AddEdge had been updated a couple months ago, so I'm assuming you are running the most recent version.