Vanishing Song Stones

Back in January I seemingly randomly had a song stone in Wind Temple disappear.  I forgot about it shortly after as I thought it was due to a cheat I had recently started using or just a Dolphin issue. This can be seen here.
http://www.twitch.tv/chaotic_ace/c/5827870

Anyway, yesterday Gymnast had the same stone disappear during a run. Here is the past broadcast. Skip to 4:54:26.   http://www.twitch.tv/gymnast86/v/27873830

In Gymnast's run he fell somewhere you're usually not supposed to, and save warped to recover. He then stored a chest different from the one we currently use (although we used to use this different chest before the one we currently use) and upon arriving at the final room in Wind Temple, the stone was gone. He ended up stopping the run and investigating further. It turned out that he had unloaded/removed ALL song stones from the Wind Temple AND Earth Temple, including the ones you need to initially break to gain access to the temple.

This leads to the next major note that needs to be taken in to account. It was discovered that the stones blocking the entrance to the dungeon were gone by going to a completely different file that had not entered the Wind Temple yet. Whatever sort of temporary flag that was set persists until you return to the Wii menu and reload the game. Saving the file after unloading the stones, returning to the Wii menu then coming back placed the stones back where they are supposed to be.

We figured that save warping in the room Gym did with storing that specific chest he did set some sort of temporary flag. Unfortunately it is nowhere near this simple. Both SVA and I were able to duplicate this without the save warp to "set the flag".

Cryze and SVA messed around with doing certain things in the dungeon to get the stone(s) to disappear and they both had very different results. SVA was able to get it with killing X enemies and voiding in a certain room, where as Cryze was unable to get it with voiding and killed different enemies. I was able to get it without voiding and without killing anything. It only ever seemed to work when we had chest storage.

Something else that may be a factor (but is very unlikely) is Makar. In the room of Wind Temple that you spawn in upon loading a file saved in it, you can pick up Makar even if he is not there visibly. We refer to this as "fake Makar". This can be found in the past broadcast from Gymnast that I linked if you care to go back a little bit and search for it, or you can see it here near the beginning of this video. https://www.youtube.com/watch?v=-7v3fu6U-hU

Using fake Makar removes the real Makar from his jail cell. When Makar is in his jail cell he is able to talk to you when you get too close. I've been able to get it with having talked to Makar. Gymnast did not.

We're not really sure yet what causes this but we know some sort of temporary flag is being that that removes all song stones. Chest storage seems to be required and whatever else is needed is affected by what you do in the dungeon. Personally I wouldn't completely rule out the save warp with chest storage thing but it doesn't seem too likely that it is needed.

This game is stupid.