When a branch project is orphaned, setBranch(Branch.Dead) is called, which causes it to appear in strikethrough text in its view (ItemColumn/column.jelly); be deletable (BranchJobProperty.decorateACL); and suppress new builds (BranchJobProperty.isBuildable).

None of this seems to work in the case that the whole repository folder is orphaned. Based on my readings of the above implementations, it would suffice for ProjectNameProperty to include a new orphaned field (or perhaps this deserves to be a new AbstractFolderProperty<MultiBranchProject<?, ?>>); OrganizationFolder to override orphanedItems to set this field, then set Branch.Dead on all existing branch projects; all other code which might add branch projects (reindexing or event support) to also set Branch.Dead when this flag is set; and make MultiBranchProject.getACL not suppress Item.DELETE when orphaned.