Arranger Track issues after flattening

Working on a tune with an arranger track. Two things seem to be issues after flattening.

  1. One MIDI track had some chords from a different section of the song. Not a terrible problem, but…
  2. I flattened to arrangement to a new project. Cubase starts the new project and asks if I want to activate it. I say ‘yes’ and start to work on the new project. I save the new project and select ‘Close’, assuming I would go back to the original project, which is still open. Instead, Cubase closes without saving the original. When I open Cubase again, I get the window asking how I want to start Cubase - with or without preferences, disabling 3rd party plugins, etc. - as if Cubase crashed. What’s up with that?

It must have actually crashed during the quit procedure.