Not sure if you have the same issue I had but....
I had a very similar issue. For me it was how the 2nd partition was formatted. After setting up with Hekate and everything working great I then reinserting the SD card into my pc (Win10) it would corrupt it somehow. Windows actually never asked me to format the card when reinserting like it should have. I used AOMEI partition assistant to format my partitions for EmuMMC initially. If both partitions mount when putting into your computer and the 2nd is viewable but with an empty folder, then you have the same issue I ran into.
I’m sure there is an easier way to fix with out starting over but that’s what I decided to do. What I did was during the setup of the second partition was choose logical partition and not primary partition. Now I can remove the SD from my switch and put in pc without issue. This was through trial and error to find what would work. So reinserting into pc wouldnt corrupt the SD again. Although I don’t put the SD card in the pc anymore, there is no reason to do so with usb install for .nsp and FTP and NXmtp for file transfers. Theres probably a better way about fixing your issue but this is what got me backup and running.
