My first NESC has been flashed 30-40 times (lots of tinkering). My second one has been flashed maybe 5 times. They both have the same issue (they've both been flashed from the same Hakchi config), so the only common denominator is the software (Hakchi, cores, ROMs).
Here is a common occurrence. I'll be playing Legend of Zelda for example, I will do a battery save, then press down+select to exit. The menu appears for about a split second, and then the screen goes black. If the LED on the NESC stays on, then it will eventually reboot, but the battery save I thought I had saved will be gone (if there was an older one, it will still be there) and there will be no suspend point. If the LED goes off, then I have to unplug the unit for it to work again. Sometimes when I push down to access a suspend point, the NESC will reset or crash entirely.
I tried the same thing with Chrono Trigger. I did a new battery save (saves are numbered, so it showed 64 saves in-game). I exit to menu, system flickers and reboots. I boot up game, and it shows 63 saves, not 64.