This is not an issue. That’s how retroarch works. The in game save is only written to disk when you properly close the game, via the menu+start shortcut, via the retroarch quick menu or via the sleep to shutdown function.
Unfortunately, you can’t recover a save that was never written to your storage.
Pressing reset or losing the battery charge while sleep both have the same outcome: you hard cut power to the running system/game and nothing is shutdown properly, so on top of not writing your saves to disk, you can even corrupt system files.
These devices are not smartphones with proper hardware that supports advanced sleep functions as we’re used too, so it is best not to rely on sleep for longer periods of time.
That can also be prejudicial for the gameplay, as if you never properly close the game and relaunch it, there’s a big chance that the emulated console ram will overflow, also breaking your playthrough. Again, nothing to do with muOS, that’s true even for real hardware, it is not an emulation quirk. It is just more commonly seen in emulation because you would rarely leave a real console on for more than 20 hours. 
There are a couple of routes you may take to have a similar experience but prevent the losing of your data from happening in the future:
Use the sleep to shutdown function instead of sleep until wake, that way after the designed amount of time, if you’re not using the device again, the system will automatically shutdown, saving your current in game save to disk. You can pair it with the resume game boot option, so when you turn on the console, it will boot directly to the game that was being played when shutdown. You can also enable auto load state and auto save state in retroarch, so when it shuts down it create a save state of that point, and when you turn the console on, it boots to the game and loads that state, and you’ll be in the exact same state where you left, as if you just had the console set to sleep. To do that open retroarch via the applications menu, go to settings>saving and turn on the auto save state and auto load state options, then get back to retroarch’s main menu and go to configuration file and save current config.
Another option you can tweak in retroarch to assure you’re in game save is sporadically written to disk even without closing the content is the SaveRAM Autosave Interval in the same Settings>Saving menu in retroarch. This is not the best option as it will consume resources while playing and wear out your sd card faster than really necessary, but if you set something like a half an hour time it may not be a big hassle.
Sorry for the long ass essay, but I thought having it all set out in one post can help future users with similar issues to understand what’s happening and find alternative paths. 