Okay, here's how you can verify the value. Take a look at this value in your database.
select name, defaultValue from windchill.PreferenceDefinition where name='saveas.replace.w.ws.content'
Interestingly enough, my XML file value is set back to 'false'. I'm thinking this is due to multiple upgrades and CPS patch installs. Regardless, the database value seems to "win" (at least until load from files is run again.)