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I've checked the Mini-Breakout schematic and none of both LEDs can be turn off permanently. The DS1 LED is controlled by the BSS138 transistor which is always active, so the LED remains always ON. The BSS138 transistor is controlled by the RESETOUT# pin of the Edison module. The RESETOUT# is an output pin that will set LOW each time there is a system reset. So the only time when the DS1 LED is off is when a system reset occurs. After that, the LED will be ON again.
On the other hand, the DS3 LED is controlled by the !CHRG pin of the BQ24074 IC , which is a battery charger and also the voltage regulator that provides the proper VSYS voltage level to the Edison module. This LED will be OFF when a battery attached is fully charged.