DISCLAIMER: Only try this if you understand what I am explaining.
Don't completely erase the microSD card yet, back it up first (Copy all the files from the root of it to somewhere safe). Do you have an emuMMC folder on the root of your card?
If so, DON'T recreate, format or partition the card, don't do that part of the guide. Since it's backed up up now, try just deleting these folders on the microSD:
- atmosphere
- bootloader
- switch
- hbmenu.nro
Now follow ONLY THIS PART OF THE GUIDE:
https://nh-server.github.io/switch-guide/user_guide/emummc/sd_preparation/
Stop after you do that part since you probably have an emuMMC. RCM and inject the Hekate payload. Choose Launch, and then choose Atmosphere FSS0 EmuMMC. See if your switch boots into your emuMMC. If it boots, install the SIGpatches. There are many posts on how to do this from me and from many others.
This is a good lesson as well going forward. Ask yourself, from my setup, what can I live without, in my situation the biggest thing I want back is my software and my saves, dosen't matter if it's home-brew or otherwise, those are the things I need. So I have backups of that and my saves. I can LOOSE everything else, because I can quickly replicate everything else, and be running again. I can't quickly replicate all of my collected software and saves. So backup, backup, backup.