If they discharge too deeply the inbuilt protection circuit won't allow the charge current in. It's a safety setup to prevent excessive heating during charging as the inrush current can be quite high at deeply discharged states. You might be able to trick it into accepting a charge and it might come sort of right, but generally at that point they are damaged to some level. Google tricking the lithium ion batteries and getting them to accept a charge - I've tried it a couple of times but without much joy. Had a few come back to life but never as good as before.
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