A bit rare problem.

1. Let we have two projects linked to one SCM repository (same filesystem path to the checkout).
2. Let we have issues in those projects references by changesets. They can be seen at 'Associated revisions' tab.
3. Delete one repository from the project settings
4. After this, all issues are unlinked from changesets (issues.changesets is empty).

Expected:
Issues are linked to changesets.

Actual:
All issue-changeset references are lost.

I think scan_changesets_for_issue_ids must be called after removing repository that is linked to more than one project. I called it from the console and it helped.

Environment:
  Redmine version                4.1.1.stable
  Ruby version                   2.5.5-p157 (2019-03-15) [amd64-freebsd12]
  Rails version                  5.2.4.2
  Environment                    production
  Database adapter               Mysql2
  Mailer queue                   ActiveJob::QueueAdapters::AsyncAdapter
  Mailer delivery                smtp
SCM:
  Subversion                     1.12.0
  Mercurial                      5.0.1
  Git                            2.22.0
  Filesystem
Redmine plugins:
  easy_gantt                     1.12
  redmine_autoclose              0.0.4
  redmine_autoprogress           0.0.1
  redmine_extended_watchers      0.0.2
  redmine_group_manager          0.3.0
  redmine_issuepoke              0.0.5
  redmine_mail_reminder          3.0.1
  redmine_pdf_wiki               0.0.10
  redmine_priority_order         0.0.2
  redmine_timelog_timer          2.0.1
  redmine_timesheet_plugin       0.7.0
  redmine_wiki_gchart_formula    0.0.5
  redmine_wiki_notes             0.0.4
  redmine_wikipub                0.0.13
  redmine_ximcify                0.0.5
  redmine_xipaycheck             0.0.6
  redmine_xiweeklyplan           0.0.2
  redmineup_tags                 2.0.7
  sidebar_hide                   0.0.8
  spent_time_closed_status       0.0.7
  spent_time_warning             0.0.3