This sounds like the battery connector might have sustained some damage. It's extremely common fault when doing any kind of repair on an iPad.
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Image above is of the underside of the battery connector and the thin little pins usually carry data about the battery and its charge status. One could be slightly bent, especially if you inserted something here to isolate the battery from the board during the screen replacement. See if you can tell without taking the whole board out. But ultimately you might need to.
The big fat pins in the middle of the connector are for power and ground. So thee battery may e charging totally normally, but the iPad would have no idea if one of the small pins was not connecting properly.