You could close and reopen NERDTree or simply hit r to refresh the current directory’s listing or R to refresh the root directory’s listing .
Do you see “Press ? for help” at the top of the NERDTree window? It means that you can press ? for help. If you do, you will see an exhaustive listing of NERDTree shortcuts. That’s neat.
More generally, many plugins have a thorough documentation that you can access with :help <pluginame>.