I can mostly answer for the guest-advanced shader pack. If the latest’s version content is copied into the crt folder, then you are good.
Updating Slang shaders resets them to a prior version. Isn’t optimal in some cases. This doesn’t alter or update Sonkun’s presets etc. They are not directly related with “slang-updates”.
MegaBezel situation is a bit different, as independent adapted shader instances are used for this project. If you are ok after updating slang shaders via updater, then it’s set.
Saved presets (you own saved tweaks) aren’t affected by slang shader updates via updater.