MHRB/NaOH can stay for days/weeks..
but separatory funnel wont help you there, friend... separatory funnel is good for A/B for not for STB, because the sludge at the bottom sticks to the walls, so even if you are able to drain it out and not block the funnel with the MHRB sludge, the naphtha will not come out clean
best to do is to crudely separate the top layer naphtha (even if a little of the bottom liquid comes, no prob) to a tall and thin container... then, with another pippete/baster (or clean the one you just used), you can much more accurately make the separation because being a tall thin container, the layers will be thicker and more distinct.. then in this second part, only separate what you can do accurately, and the last bit of naphtha just pour back into the main container for next pull
Also, better not filter the crystals as you did.. instead, pour out the naphtha (and reuse for next pull), and put the container with the crystals that are stuck to the side upside down, but with some support so it stays at an angle and air can come inside.. Put a fan in front to make big air circulation.. This way any any remaining naphtha will drop out/evaporate, instead of warming up and melting the crystals as it probably happened to you. Then once its totally dry after a few hours you can scrape it out.
and also remember if just very little crystals come out, you should evaporate your naphtha half the amount or more, and stick it back in the freezer again