If I've interpreted your requirements correctly I think this script will do what you want. Let me know if I've misunderstood something.
1000.xxx and 1003.yyy will be deleted. 1001.yyy and 1002.xxx will remain because they have matching .aaa files.
MagicExt = ".aaa"
Function OnClick(ByRef clickData)
Set cmd = clickData.func.command
cmd.deselect = False
Set setMagic = DOpus.Create.StringSetI
For Each file In cmd.files
If file.ext = MagicExt Then
setMagic.insert(file.name_stem)
cmd.RemoveFile(file)
End If
Next
For Each file In cmd.files
If setMagic.exists(file.name_stem) Then
cmd.RemoveFile(file)
End If
Next
' remove this loop once you're satisfied the script works correctly
For Each file In cmd.files
DOpus.Output "Will delete: " & file
Next
' uncomment this line to delete for real
'cmd.RunCommand("delete")
End Function