The issue is caused by r20766 which was done for #34032. The form parameter (project_issue_tracking) was changed without processing it in the controller.
The other values for custom fields and trackers are set correctly as the name of their input fields is hard coded in this view.
Started PATCH "/projects/ecookbook" for 127.0.0.1 at 2021-03-30 16:15:05 +0200
Processing by ProjectsController#update as HTML
Parameters: {"utf8"=>"✓", "authenticity_token"=>"rLc3tuqdXLulwVWSOqG0OhFdFyMT13ycZWYXRpWU2ggMIjQT1sN5KdG3eGp21rx81_LtHLSBg2Z46tSgEm2E9g", "tab"=>"issues", "project"=>{"tracker_ids"=>["1", "2", "3", ""], "issue
_custom_field_ids"=>["9", ""]}, "project_issue_tracking"=>{"default_version_id"=>"3", "default_assigned_to_id"=>"3"}, "commit"=>"Save", "id"=>"ecookbook"}
At the moment I don't know what's the best way to fix it. Reverting the patch or modifying the controller to additionally save the values of the second parameter. The last seems to be the cleaner option to me.
@GoMAEDA, @MariusBALTEANU I posted this comment accidentially in #34988.