Its hard to brick a Switch even when its hacked. So its highly unlikely you will cause irreparable damage by using a RAM editor. Just make a backup of your eMMC once you hack it and you can recover from 99% of all bricks.
How is your SD card formatted? Also have you tried deleting all of the files and downloading the newest files from their respective GitHub pages?
This is the one for Atmosphere and
here is the page for Hekate.
You have to delete the old /atmosphere folder then put the new one on the SD card. Atmosphere doesn't support dragging and dropping the files when updating the CFW.
Shallowsea is probably just the bare minimum files needed for using Hekate so if you don't boot Atmosphere using Hekate, you won't be using Shallowsea anymore. Which means you will have to boot Atmosphere using fusee instead of Hekate.
As far as I'm aware, there is no known way of modifying the play activity of games without using NX-Activity-Log.
But do you have a file called package3 inside your Atmosphere folder?
I would highly recommend reinstalling them with
TinWoo Installer. Its what I personally use and I never have any issues while using it.