Each shadow year will take its start from the Official Game save. So even if you were to take a different research route for your shadow turns in year 20xx, your shadow turns for year 20xx +1 would start from the state of play of the last Official game turn. You will not be running a shadow game that departs from the official game for very long. Make sense?
Don't worry about asking questions, better to understand the water temperature before we jump in.