You can give OS3.9 partition the highest priority so that if you don't choose anything it will load OS3.9. If you want to boot from another partition with a lower boot priority then you need to 'disable' that OS3.9 partition in the early startup menu. About those things that stay in the memory after a reboot, it may be better to switch off your computer if you want to boot up Linux (for example) after you runned OS 3.9 ...
