Can I turn off my Magic Mouse 2 when I'm charging it's battery through the cable?
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Yes, you can turn it off while charging.
However, according to Apple:
For the fastest battery charging performance, be sure your device is switched on when connecting the Lightning to USB cable.
Source: Recharge the built-in battery in your Apple accessory
Yes. I normally turn mine off so my computer, which is nearby, won't acquire it thru bluetooth.