The difference is ground fill is connected to all traces that are part of the ground seeds you selected. You use ground fill usually to reduce noise between traces/components. Copper fill is simply filling the unused space with copper and serves little purpose other than reducing the amount of copper that has to be removed from the board during etching/milling.
You say missing traces but again from you previous picture they are not missing but rather they are all now part of the ground plane. If you use a multi-meter to check continuity between ground pads you will see they are still connected as before doing the ground fill and nothing has been removed.
Now if you have selected the wrong pads as ground fill seeds then your board will not work and you will need to clear the ground fill seeds and set them up again making sure you only select pads that are part of your ground (v-) net.
