Yup, if you touched +4.5 volts from a battery (able to deliver lots of current) to the shell of the USB connector, then it would burn the ferrite bead.
The board will work fine without that part, but the USB shield won't be connected. That probably makes no difference functionally. It's only meant to help the shield contain lower frequency noise, without letting it act as an antenna for higher frequencies. But usually the shield is connected directly to ground at the PC side anyway.... and even if it isn't, the worst case is probably only a tiny bit of random radio frequency noise emitted, but only when a USB cable is plugged in.
Do be careful with those wires. If 4.5 volts from a strong low-impedance source touches elsewhere, it could destroy the chip and ruin the board.