I’m really happy you got good data out despite the logging issue! Yes, new appliances pay for themselves quite fast :)
Regarding the meat of the question: If the meter keeps trying to log as the battery dies, I think it’s possible this could cause the filesystem corruption you saw. The SD card draws the most power of anything on the meter when it is writing, so my hunch is that when the batteries are near death a write event might cause brown-out. I have some code in the firmware to prevent this problem in normal use but it’s not tested against all SD cards and circumstances (if the batteries are cold, they sag more, stuff like that).
Regarding battery levels: the indicator in the app is quite rough: 100% means 3.0V or more, 0% means 2.0V or less, and it’s linear in between. The meter shuts off around 2V.
Estimating battery life while logging: What was the logging interval set to? The longer the logging interval, the better the battery life. I am going to change the default so it’s no longer 1s, because this is actually quite battery intensive. Since the ADC needs to settle for at least 2 seconds before giving a good reading, a 1s logging interval means the ADC never turns off and draws quite a bit of power. Also, was the meter in the fridge/freezer when performing this logging? Cold temperatures also reduce the amount of power available from batteries (this is reversible when the batteries warm up though).
Hope this helps with diagnosis, I’d love to see logs if they are available :)