I frequently run CC manually, Health check, Skip to start health check.
Before I click 'Skip...' I frequently first click on Option, Cookies, Right click the left column cookie listing and select 'Intelligent scan'.
I started doing this months ago after realizing the the cookie clean was clearing important login/setting cookies for a variety of websites. The Intelligent scan seems to mostly fix the problem.
But I cannot find a setting that embeds this choice into the software for whenever I run cookie clean or cookie clean is a part of a larger CC automated function.
Health Check is meant to always use and only use it's own cleaning rules.
It doesn't respect any of the Custom Clean ticks/unticks; and I'm pretty sure that it doesn't respect any changes you make to 'Cookies to keep' either.
(I know from my own testing that it doesn't respect Custom Clean 'Includes' or 'Excludes').
If you want to be sure that your 'cookies to keep' are respected then I would always use Custom Clean and not Health Check.
You can also add further 'cookies to keep' that are not covered by 'inteligent cookie scan'.
See this for more information about keeping all or particular cookies: