Atmosphere by default has something that'll automatically disable the gamecart slot from working to prevent fuses being burnt in there. So then if you were to go to a lower firmware, you can use your gamecart slot still. The issue with this is that if you don't care about downgrading and want to use your cart slot, you can't without disabling the block. Use this page for how you can enable the slot again.
Note: Disabling the block does run the chance of burning its fuses, so if you want to restore to an earlier firmware, you most likely won't be able to use the slot on that firmware anymore (only newer ones).
Step 1. Hook your SD card up to your computer (Hekate USB tools, memloader, however you do it.)
Step 2. Navigate to <sdroot>\atmosphere\config , and open the BCT.ini file with a text editor (Notepad++ is my go to.)
You can either force enable the nogc option, or disable it. In our case we want to disable it, so you append to the bottom of the file nogc = 0. Your file should look like mine here, the very bottom at least.
Step 3. Save the file, eject your SD card and boot your switch with your payload. You should now be able to play gamecarts just fine.