How to migrate a project to yarn flat mode?

We have a rather comprehensive ember-cli project with many dependencies, which wie manage with yarn. Now we'd like to convert it to yarn flat mode but yarn wants to convert all dependencies to flat mode and asks for dozens of dependencies for the version to use. Sometimes this is simple like choosing between 1.0.2 and 1.0.4. But there also cases where I have to choose between 0.0.3, 1.0.19 and 2.2.1 and whatever version I'll choose, something breaks. Due to the fact that yarn always converts the whole project and all dependencies it's rather complicated to debug which of the difficult version choosings actually breaks the whole app.

Is there a way to do the migration in a "mixed" mode where some dependencies are managed flat and some not? This way I could migrate a single package to flat mode and test the app, run specs and so on and continue with the next package.