After changing the first value, the second does not seem to be written to disk. For example, I played with 3 plugins that need updates:
Observing the config.yaml, only the first gets an entry under plugins.softwareupdate.checks:
checks:
eeprom_marlin:
disabled: false
EEPROM Marlin is able to be changed between true/false, but the others never appear. They do persist across reloads of the Web UI, so I think it is just the writing to disk
Settings would stay as they have been set
Reverted to default (enabled)
Unable to test, since safe mode means plugin version checks are disabled.
1.5.0.dev271+gf291fa898
OctoPi 0.17, but with development environment installed.
N/A
New Edge, 85.85.0.564.70
octoprint.log
^ this is a bit long, but no error was produced when the API endpoint was called - it seemed to think everything was successful. At least as far as I could see.
N/A
I have read the FAQ.
I have a feeling that this might have been an issue introduced in a subsequent commit (as in, since muting notifications was introduced), since it doesn't work on my windows machine at all, and the report above was from my dev RPi, where I used the feature when it was first a thing on maintenance.
Ok so I have played with this on and off, and some steps to reproduce seem to be either:

Pretty sure that this one and #3765 have the same underlying cause, as both those features are implemented in the same endpoint in which I've observed some issues with config caching in self._settings that I'll need to investigate further.
Should be fixed on maintenance.