Solutions for Introducing a new Entity In Between An Existing Association
For such a structural change in your data model you will have to go “all in”. You can’t model the same entities in 2 ways. As you correctly observed, it will lead to endless grief for years.

That means your “old” view of the world will have to adjust.
Have you considered creating a single order to contain all batches for existing projects, and name it “Migration Order” or something meaningful? Your application may choose to ignore it when presenting, or not. This will maintain a unified hierarchy.