Get a clean SD card and install only the Hekate/Atmosphere files.
This will help to determine it if is somehow related to your original card.
Ejecting your SD card might have messed up the card, especially if it is formatted with exFat.
Another check for RCM is using Lockpick_RCM.
This should be able to boot without an SD card.
Also make sure to turn off the Switch by pressing the power button 15 seconds and then try to boot into RCM mode (volume up + power button).