Maybe this helps someone.
I had a similar issues on Rearmed core on RetroArch on the switch.
The game would sometimes get stuck in a state if you pressed pause or inventory the game would freeze.
It happened to me in certain sections of the game
on a water level with crumble blocks above spikes after a slide (I somehow wondered back and did more things and I fixed it).
on the last room of the barkhang monestary after putting in the prayer wheels. It forces you to put in an item and open up the inventory and freezes
I did manage to save the game before this in the pause menu book (you have to do it before getting into that state where pause crashes the game). Copy the save file .srm, play it on PC (same emulator but x86) finish the level, save and reload onto switch (or your retropie).
Sadly if you rebind quicksave and quickload not to pause the game as a workaround it will eventually force you to open the inventory and freeze the game.
Not ideal but possible not to loose all progress and potentially keep playing on