I never knew how to keep phenols in the room.
Just keep them away from small children and naked flames
Seriously, the method of shutting down the game is safe (I've done it hundreds of times) but since the last update, the items like Neptune, Emerald or Mercury don't show up on the "found items" list even if you have unearthed them until you click on "close".
So you may have found the item but don't know it.
It took me about 150 attempts clearing the Hunting Room/ Hallway to find "Mercury" and I had to buy at least 6 native idol summoners as I was never sure if I'd already got the thing.
After sending another shitagram to GI (about other bugs) yesterday, I closed the rooms out and lo and behold, Mercury dropped.
So the good news is that my iPad is still in one piece and should any of my Manor friends want to "borrow" Neptune, Emerald or Mercury, then I'll happily send. They've currently orbited the Earth more frequently than the Sun!