Is this working in the Waveform or Multitrack editing view? If in the Waveform view then yes they will disappear as soon as you have applied the effects in the Rack since Waveform editing is destructive. If you want to re-use the same effects settings on another bit of audio you will have to Save the rack settings as a custom Preset. But at the same time remember that once the effect is applied it becomes part of the file so you cannot undo it once the file is saved. However you do have the opportunity to Undo the application of the effect by going back into the Undo History before you finally save the edited file.
In the Multitrack view editing is completely non-destructive so you can go back to the Effects Rack and change the effects settings to something new.