Some games are still having problems with the saves even with yesterday's build.for retroarch the save files are located in /retroarch/cores/savefiles/ unlike standalone the file extension needs to be replaced by .sav (i.e. 0413 - Tetris DS (Europe) (En,Fr,De,Es,It).nds -> 0413 - Tetris DS (Europe) (En,Fr,De,Es,It).sav).
The initial release of the switch libretro core with JIT, suffered from the issue that it couldn't always create the right savefiles on it's own, but that was fixed already days ago, try updating the core.
Dawn of Sorrow, Order of Ecclesia, Kirby Super Star Ultra and NSMB refuse to detect my saves I've been using on TwilightMenu++ and my flashcard while all my other games detect them without issue (though they do seem to create a new one just fine), and Portrait of Ruin just flatout refuses to detect and even create a new save file.
All of this on a Switch with the March 19th build.