Doubt anyone else here experienced the same, but maybe someone has run into a similar situation and can help me understand what happened.

I was casually playing through the game, reached Area 4, explored it all or as much as possible anyway, and hit a wall since I couldn't figure out where else to go to progress, so I got to the top of the elevator room and stood on the top platform for a while, thinking of what I hadn't tried to do yet. I then got distracted and didn't look at the screen for about 15 seconds, only to find out when I looked back at it that the screen was flashing with black and pink stripes, and at the center there were two flickering sprites of what seemed to be bosses I guess that I couldn't quite recognize. I couldn't do anything on that screen, tried to press everything I could, and "start" was the last button I pressed; it brought me back to the first room of the area as if I had normally died, but the room was partially glitched and the game completely frozen, and I noticed that all my stats (level, exp and HP notably) got reset as if all my progress was lost. I then reset the game, selected "continue" and the game brought me back to Area 4 but all my progress was indeed gone, making it basically impossible to move on and eventually try to replicate whatever happened.

None of what I just described was recorded unfortunately.

If you guys have any idea as to what could have possibly happened, feel free to share it, otherwise thanks for reading if you've made it this far.

Some of the hidden areas are ridiculous, you need to shoot them with certain guns, and use certain crystal powers. If you get lost, try checking the walkthrough on gamefaqs or the full game speedrun on the board which is essentially glitchless.

As for the glitched area, I don't know what happened there, sorry.

I can't say that I've ever run into any of this. Sounds like a hell of a glitch, though.

Might be irrelevant, but what were you playing this on emulator or console (and if on console, on original cart or PowerPak/Everdrive)?

I was playing on Everdrive for Famicom, English translated version of the game since it was my first playthrough. It was very random and absolutely unexpected of course, really wish I was recording, not cause it could be any useful to the run probably, but just because of how weird it looked. But yeah, thank you all for taking a look at this :D