Under normal conditions, there is no need for you to call stop mining manually at all as the node calls this method instead of you during the shut-down process. However normal conditions are not always present and these few edge cases when you must call stop mining manually are described here
If node shut-down process fails
When your node is shutting down, it automatically calls stopMining function on Lition Registry contract.
In case something unexpected happens and stopMining is not called or other nodes did not receive AccountMining event with your account, you might end up in a situation when you are still registered as active validator in Lition Registry contract but in reality you are not mining anymore
It is no big deal as you are going to be automatically removed from the list of active validators in Lition contract and unvoted by nodes after 2 notary windows during which you did not mine no block, but still you can and you should take care of this process by yourself and call stopMining manually in Lition sidechain manager.