The chemicals inside batteries don’t disappear (conservation of mass and all that), they just bind and unbind with other molecules to push and pull electrons from the other half of the battery via the 2 terminals. Charging and using the battery makes the 2 (or more) reactions go back and forth between a few states. The lithium is still there in some state or another. It just(over simplification) needs to be put through some other chemical reactions to return it to a pure form for reuse.
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