According to this thread I can disable this thing altogether but this battery-critical-power-down not always happens. Is there a way or terminal command that can stop the power manager shutting down my computer when that infamous message box pops up?
Command line option:
As far as i know, the computer can be set to either Shutdown, or Hibernate (free space/swap space providing).
If Hibernation is something you consider an alternative, then you should be able to change it in the Power Manager.
If not, then the system is trying to protect it's hard disks/memory from corruption, and it would be very difficult to disable, and is something i can't help with.