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It may not be a problem. If the battery is so low that the system won't boot up, then the USB limits the charge current to something very low for safety (because that is usually negotiated with the OS). It takes a long time to charge at that low current. The best thing to do is what you did: charge it enough to boot the device, then reboot and continue charging with the live system to get a higher charging current. Ideally, you should recharge before the battery gets so low that the system won't boot up.
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