If you are using Atmosphere, you can boot the stock emuMMC via Hekate to have the emuMMC online as safely as possible. As for a guide, you can find one
here
You cannot boot Atmosphere and ReiNX on the same SD card if the console's firmware version is at least 7.0. That is because both Atmosphere and ReiNX have their own sept folders needed to boot their respective CFW meaning you can only boot between ReiNX or Atmosphere after firmware 7.0.
I would highly recommend you link a Nintendo Account on the console as soon as possible since certain content requires a linked account such as the NES application, Super Mario Maker 2, Bloodstained, Mortal Kombat 11, Stardew Valley, etc. Also you do not need Incognito if you are using a DNS server to block Nintendo traffic. One or the other, or even Airplane Mode/removing Wi-Fi settings, is sufficient.
Unfortunately, the only thing I can recommend is temporarily updating your sysMMC to the latest firmware to get the latest keys via Lockpick_RCM. You can simply use the homebrew application ChoiDujourNX to update your sysMMC firmware without burning fuses so that you can restore your NAND backup without any issues. Although you typically do not need keys unless you are converting files on your computer or datamining games. You can even find the keys on Google if you know where to look.
It means there might be something wrong with your USB cable, computer, or both.
Do you have an Android or rooted iOS device that you can try sending a payload with?