The 'Trackers' in Health Check are not what you are thinking of as 'Trackers'.
It is just a catch-all name that Health Check uses for Cookies, Browser History, and Temporary Internet Files. - Things that have 'tracked' what you have done whilst browsing.
So your browser history is a 'tracker' from that point of view.
You can see what 'Trackers' actually are if you click on 'Privacy after running Health Check's analyze, but before 'Make it Better'.
So if you wanted to keep the History but clean Cookies and Temporary Files then you could untick history like I have here - the problem with that being that you have to remember to untick it each and every time that you run Health Check.
It also cleans any/all browsers that you have used, so you can't clean/save history for one but not for another.
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In Custom Clean you have more control over what does and doesn't get cleaned, so if you want to keep the History you simply untick it and Custom Clean will leave it alone.
If you want to keep it for one browser but not otheres then you can set it diferently for each browser.
Custom Clean remembers what you have ticked/unticked for each browser (and the other sections), so you only have to do it the once and it's then used every time.
So it isn't a question of what to tick to clean 'trackers', they'll get done anyway (unless you untick the particular catageory they are in).
It's a matter of unticking the ones that you want left alone.
PS The things that are unticked by default are like that for a reason, they are things that you wouldn't normally want to clean but just might at some time. eg. You wouldn't want to delete your browsers Saved Passwords everytime you run Custom Clean so that's unticked by default, but there may be a time when you do want to delete them all at once so the option to tick it is there.
You can set Custom Clean to be the Default cleaning method that CCleaner shows you when you open it:
Go to Options>Settings and change the CCleaner Home Screen to Custom Clean.
As for the question about things coming back straight after a clean - that is normal for any computer.
See the link in my signature below this for an explanation of what they are, and how you can stop some of it happening if you want to (you can't stop it altogether, that just the way computers work).
If you can't see my signature then here it is as well: https://community.ccleaner.com/topic/52668-tracking-files/?tab=comments#comment-300043