diff --git a/app/models/submission.rb b/app/models/submission.rb
index f97afb86..e049a966 100644
--- a/app/models/submission.rb
+++ b/app/models/submission.rb
@@ -205,7 +205,7 @@ class Submission < ApplicationRecord
     begin
       runner = Runner.for(user, exercise.execution_environment)
       files = collect_files
-      files.reject!(&:reference_implementation?)
+      files.reject!(&:reference_implementation?) if cause == 'run'
       files.reject!(&:teacher_defined_assessment?) if cause == 'run'
       Rails.logger.debug { "#{Time.zone.now.getutc.inspect}: Copying files to Runner #{runner.id} for #{user_type} #{user_id} and Submission #{id}." }
       runner.copy_files(files)