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Yes, the clock stops working if the Edison is turned off. In order to have the clock working while the Edison is powered off you need to power V_VBAT_BKUP. According to the Hardware guide you should connect an external power source to pin 23. The voltage and ampere values are programmable. The default settings are 2.5V/10uA. You can see a discussion about that here I need "V_VBAT_BKUP" pin specification . When the RTC is being powered I don’t see the need to have NTP enabled, try turning it off.
As for the log files, I’m not sure if there are some kind of timestamps that can help you tell the order of creation of the file. Take a look here SQLite Query Language: Date And Time Functions . Hopefully you find this useful.
Thank you Sergio. It seems the SparkFun blocks don’t break out or connect to pin 23, I don’t have an Intel breakout board and soldering to the header appears risky. So I’ll try to have the prototype fully powered continuously during next deployment. For accidental power loss I’ll see whether disabling NTP or regularly setting the hwclock helps.