ee-specific-lines-check failed to rebase when CE branch merged and resolved a conflict once from CE master

This was discovered in:

Messages:

=> Running `git checkout -f target-ce/jprovazn-remote-upload-destroy`
Previous HEAD position was 625b46ffe9 Fixed typo
HEAD is now at 2060533f91 Whitelisted query limits for group destroy API
=> Running `git clean -fd`
=> Running `git rebase --onto a78b1b27b86d34c00e1b0631e967d637f8a6714b 14507fd18110c6662f56709835a0d68468d7680e~1 target-ce/jprovazn-remote-upload-destroy`
error: Failed to merge in the changes.
=> Running `git status --porcelain`

💥 Git status not clean! This shouldn't happen. Please create an issue
💥 and ping @godfat to investigate.

⚠️ Git status:

M  app/models/appearance.rb
A  app/models/concerns/with_uploads.rb
M  app/models/group.rb
M  app/models/project.rb
M  app/models/user.rb
A  changelogs/unreleased/jprovazn-remote-upload-destroy.yml
M  spec/models/appearance_spec.rb
M  spec/models/group_spec.rb
M  spec/models/project_spec.rb
UU spec/models/user_spec.rb
A  spec/support/shared_examples/models/with_uploads_shared_examples.rb

I could successfully reproduce this locally, and apparently https://gitlab.com/gitlab-org/gitlab-ee/merge_requests/5719 would not be able to fix it because the cases are different than https://gitlab.com/gitlab-org/gitlab-ee/issues/5960

/cc @jprovaznik @reprazent @leipert

Edited by Lin Jen-Shin