Alright, so while playing with the GBBC today, I learned something I was unaware of previously.
When the batteries get low, it causes the system to act a bit screwy. Usually causes the console to just reset. After looking it up, I found out the before mentioned that it's the low batteries.
However, this just screwed my Link's Awakening save. It reset just after I had gotten the Full Moon Cello. So I thought I had to do it again, but lo and behold the boss was still beaten, and the Cello was gone, so I thought it saved and all was well. But no, not at all, it did save, but it shows I beat the boss, but the Cello isn't in the inventory, and I can't get into the next dungeon either, the "Moblins Attacked The Town" event isn't triggered.
It happened while I played Pokemon also, causing Shockslayr to no longer be in my party.