Swith line_item_syncer.create_new_items from deleting line item in the case of stock issue, to simply set the quantity to zero. This makes things easier later as the line item is already present if the user tries to change quantity of the subscription_line_item

app/services/line_item_syncer.rb

@@ -35,8 +35,8 @@ class LineItemSyncer
                                               skip_stock_check: skip_stock_check?(order))
       next if skip_stock_check?(order) || new_line_item.sufficient_stock?
 
-      order.line_items.delete(new_line_item)
       add_order_update_issue(order, new_line_item)
+      new_line_item.update_attributes(quantity: 0)
     end
   end
 

spec/services/order_syncer_spec.rb

@@ -500,7 +500,7 @@ describe OrderSyncer do
           expect(syncer.sync!).to be true
 
           line_items = Spree::LineItem.where(order_id: subscription.orders, variant_id: variant.id)
-          expect(line_items.map(&:quantity)).to eq []
+          expect(line_items.map(&:quantity)).to eq [0]
           expect(order.reload.total.to_f).to eq 59.97
           expect(syncer.order_update_issues[order.id]).to include "#{variant.product.name} - #{variant.full_name} - Insufficient stock available, only 5 remaining"
         end