In Fantasy LoL, if your starting player doesn't play, you will receive points from the player that replaced them. This replacement will be reflected in the matchup screen interface once the game begins.
In addition, nobody in your league will be able to pick up the replacement player for your starter so long as they reside on the same team and play the same position. This functions the same during the draft, in that drafting a starting Mid Laner for CLG means that you effectively also own all CLG mids, and nobody else can draft another CLG mid during the draft.
This way, you will not need to worry about last-minute lineup changes.