When you’re down to your last half segment of energy, with no match in reach, you can try a Hail Mary by physically shaking the device. This will repopulate the board and if you get an auto match your energy bar will be refilled and you’ll live to fight another day.
The bar flashes just to let you know you’re about to run out
You can use the crank anytime, so long as you have more than one segment of energy remaining. That will move colors around inside a row or column.
The play through video that gogamego posted shows this off well, and there are additional instructions on how to play on the main page for the game and here: http://scenicroutesoftware.com/shift-playdate/