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I have an iPhone 5s that I changed the screen and battery, it was charging originally after repairs but then it stopped charging, could it be the pins on the logic board were bent since I had not sealed the device yet? The display is a Ifixit display and the battery is a scanditech, please help!

Do a thorough visual inspection, preferably with magnification, of the area surrounding the battery connector. There are several tiny SMD components just above the connector. Of particular importance is FL11, at the top-left of the connector. If it is missing (which can happen when you pry the connector off), then the battery state does not get communicated to the CPU and this can also cause charging issues and fluctuating readings.