Currently we have the following options for preserving settings for Flow Design
1) In Flow Design for Inventor and Flow Design for Revit, settings are preserved within a session. If you turn off and then turn back on FLow Design inside those CAD packages, settings are maintained. But if you close Revit or Inventor (ie you end the session) you no longer have those settings.
2) In Flow Design standalone, you can export an FDZ file which saves the geometry and setup. You can recall those FDZ files in later sessions of Flow Design standalone.
We have heard some feedback from users who want to save settings between different sessions of Inventor. You would be able to use Flow Design on a model in Inventor, close Inventor, and then re-use those same settings on a new session of Inventor later on. Give this idea kudos if you'd also like to see this.