Lost save on Ocarina of Time (but not file...?)

[buffalobill90]

I downloaded Legend of Zelda: Ocarina of Time recently and had just entered the water temple under Lake Hylia on the game. After downloading a new emulator today (Dolphin v1.03.2) and moving my Project64 v1.6 emulator folder from program files to the same location (i.e. I made two new folders, one for each emulator, and placed them in a new location outside program files) I started the Ocarina of Time emulation on P64 and when I accessed the menu screen my save was no longer there.

When I checked the 'save' folder in the P64 folder an .SRA file was in it named: 'THE LEGEND OF ZELDA'. I assume this is my game on Ocarina of Time (I also have Majora's Mask but with no saves on it) and I had accidently changed something when I moved the emulator files to a new location, or alternatively, downloading the new emulator interfered with P64 in some way.

I would simply like to know if it sounds like my game file does still exist, and if so, how I can play it again using the ROM.

[buffalobill90]

Just found out I've got the same problem with my Jet Force Gemini ROM: my game has disappeared. Also, the 'save' folder in the P64 folder has a new file in it: JET FORCE GEMINI.fla

This file has only appeared now that I have run the JFG emulation.

What's going on...