Each layer is assigned a leaflet ID, so you could iterate over the layers in the group using the eachLayer method and look for the ID to remove. Wrap everything in a function that you can call when you want to remove a layer by it's ID. Something like this:
var mylayergroup = new L.LayerGroup();
function removeMe(id) {
mylayergroup.eachLayer(function (layer) {
if (layer._leaflet_id === id){
mylayergroup.removeLayer(layer)
}
});
}
When you want to remove the layer with a leaflet_id of 50, you would just call removeMe(50).
BRYAN