Doron,
There is a relatively safe script in the distribution folder \JMRI\jython named "TurnoutStatePersistence.py" that handles Dick's valid concern about throwing turnouts under parked rolling stock and fulfills Roger's intent of a known starting point initialization.
If however, you are talking about a club layout with even one member who runs trains without turning on JMRI, then even this powerful script can be defeated.
When used properly, use the Edit -> Preferences menu item in PanelPro to get the "Preferences" window. Then select the "Start Up" option from the list on the left side and click on the "Add" button at the lower left of that view. Select the "Run Script" option from the popup list and then navigate to the JMRI\jython folder, which is the default choice but not if you have changed the "Jython Script Location" in the "File Locations" view of the "Preferences" window. In general pay attention to the "Scripts should be run last in most cases." message, but the "Add" function will take care of that for you.
Finally click on the "Save" button and wait for the prompt to restart. Do the restart action.
Initially, the script will alert you about a missing file with the name "TurnoutState.csv" but that is OK once.
From then on, each time you shut down JMRI, the script will write a file with the State of each known turnout, so there should be no more missing file alerts. That same file will then be read each time you start JMRI, so there is also the requirement that you have powered up the layout prior to starting JMRI.
Cliff in Baja SoCal
Roger Merritt
Ken Cameron