The whole system is based on actions triggered by Calculate. If you're worried about losing or overwriting data you've already calculated, though, there are two options you should check: the "Clear Calculated Data During Calc" boolean on Scenario properties, and the "durable data" options in api.Data.Calculate (which allows you to manage the lifecycle of calculated data explicitly, as you see fit). There is also the ExecuteCopyDuringCalc option that you can pass (True/False) if you want to be in control of when the copy happens.
It makes a bit more sense if you think of Hybrid Scenarios as a feature to help analysis (and hence, expects calculations to have been run) rather than a seeding tool.