Saves can have different formats and file extensions depending on the game. ".sav" was mainly used for save files from Gen 1 - 5, on the 3DS they where simply called "main" without an extension at all. The Switch uses "SaveData.bin" and "Backup.bin", the first is your current save while the latter is the backup used by the console incase the current save is corrupt.
Just look how JKSV exports your saves from your Switch, you will see they look exactly like this.
You should open the SaveData.bin, if PKHeX can't read it there's no data inside. Save ingame normally and stop using save states, then PKHeX will be able to read the file (assuming it is not a ROM hack that has modified how save data is stored).