I have just come across this myself. I only have the one ME open and I'm only working on one mission, going in and out of 'fly mission' testing the tweaks. I know I'm saving it because it asks me to save every time I hit the button.
Every now and then my mission name reverts back to 'New Mission', instead of the name I saved it as.
Not a biggie, just keep your eye on the bottom left for the correct file name before you save it. If you check your 'New Mission' save, you should be able to pick up where you left off.