the cave doesn't have anything in it there is a quest however for the temple if that's what you mean.
There is only one place to find glowshrooms and you should be able to find 5 of them there. There is no other place where you could lose them. So I'm not really sure why you have only 3. I heard it happened a few times, so I'll have to find the issue. It may be because save file was somehow corrupted. Were you replacing the old folder with a new one? Like putting the folder one on top of another?