Draft: Refs #456 - Ignored notification categories are not saved

Core does modify the arrays without resetting them back to Prefs.

I was investigating a test failure on the feature branch and it seems to be a regression for recent #443 fix. Essentially we create a copy of an array from the defaults trying to prevent the modification. However core seems relies on it and just modifies the array without resetting it back to the Prefs. This introduces a regression on master which is not discovered on CI due to errors cleaning which makes it using another empty array, not the default one. If to run the test alone it will fail.

References #443 (closed)