Ref for merge train removed before manual cleanup steps

Summary

We set up a pipeline running in merge requests, using merge trains. The final testing job is set to manual (used to clean up the staging area). However, this fails:

Running with gitlab-runner 12.3.0 (a8a019e0) ... Fetching changes... Reinitialized existing Git repository in path fatal: Couldn't find remote ref refs/merge-reqests/42/train ERROR: Job failed: exit code 1

Steps to reproduce

Use merge trains and

only:
  refs:
    - merge_requests
when: manual

Our configuration also has

environment:
  name: xxx
  action: stop

Example Project

(If possible, please create an example project here on GitLab.com that exhibits the problematic behavior, and link to it here in the bug report)

(If you are using an older version of GitLab, this will also determine whether the bug is fixed in a more recent version)

What is the current bug behavior?

refs/merge-requests/xx/train is deleted when merge request is merged. Git ls-remote does not list the train refs.

What is the expected correct behavior?

refs/merge-requests/xx/train should be retained, or the final manual step should be able to use some other ref.

Relevant logs and/or screenshots

(Paste any relevant logs - please use code blocks (```) to format console output, logs, and code as it's tough to read otherwise.)

Running with gitlab-runner 12.3.0 (a8a019e0)
  on shared-runner XXX
Using Docker executor with image YYY ...
Pulling docker image YYY ...
Using docker image ZZZ for YYY ...
Running on runner-RRR...
Fetching changes...
Reinitialized existing Git repository in path
fatal: Couldn't find remote ref refs/merge-requests/42/train
ERROR: Job failed: exit code 1

Gitlab ee version 12.3.6. I don't have access to run commands server side.