Lithium Ion Battery Completely Discharged. National Renewable Energy Laboratory. Colorado School of Mines Golden Colorado September 7-9 2014.

Your devices have a safety mechanism that stops that. No it is not OK to have a Li-Ion deeply discharged at all. Due to excessive self-discharge the voltage of the lithium-ion battery may be too low causing negative and negative copper foils dissolution and other risks because the dissolved copper element.
So if the lithium-ion battery in your smartphone has seen better days there are a few things you can try to bring it back to life before spending the cash to replace it.
Lithium-ion batteries will face the risk of excessive self-discharge during long-term storage especially at lower open-circuit voltages. Plug the cable into your device and connect the exposed wires on the battery to the respective feeds. Beyond that any use of the battery will reduce its life span because there are a finite number of cycles. Lithium-ion batteries can be recharged without completely discharging with no battery degradation and can withstand literally hundreds.

