It looks like most things on that board share the same ground. The largest fill areas on both top and bottom are ground planes, and most of the vias in them are there to stitch together the top and bottom ground plane. You can see one side of the LED is hooked to the ground plane, one side of the large capacitor BC1 on the top side of the board, the marked GND pin on the five-pin connector, the ground pin and the shield on the existing USB connector, as well as other things are all connected to that same ground plane.
You said the USB B port is for a flash drive, so it is intended only to provide power to the flash drive, not to accept power input there. Depending on how they did the power switching, the device might still work and charge if you apply 5V power there, but it would be better to fix it with a new micro-USB port like you were planning. I think that both transistors, at top right (Q3) and at top left (Q1) are for power switching and/or anti-backfeed functions.
My best guess is that the micro-USB port had its ground connected directly to the common ground plane, and its +5volt pin connected directly to the anode of the large diode at top-right, D1.