Yes, you can set up a scheduler using Quartz or Runnable and persist the mf qualified name and runstate in the db. Whatever class you are using for the executions in a global container so before shutdown you can iterate through them and trigger some logic for stopping them. At startup, use the db persisted mf data for reinvocation when the runtime starts again
What are you trying to achieve?
If you want run tasks in the background, have a look at using a Scheduled Event, or a Queue. You can commit data in your user triggered microflow, and have the the Scheduled Event or Queue action pick this up and work with it.
Hope this helps.