Back by popular demand, Auto-Save is now available in FlowJo v10.6 and newer. By default FlowJo v10 will not automatically save workspaces.
To turn this functionality on, simply visit the Workspace section of the preferences and choose a time frame for the auto-save to cycle (in minutes).
This will keep saving the workspace, automatically, wherever the initial save was produced.
Note: this function is not available for ACS formatted analyses.