Good to hear you got the bookmarks back.
Don't forget to follow the links above and make backups now, just in case.
I had guessed that you had Health Check set as the CCleaner default cleaning method.
(It may have got set that way when you updated to v5.64).
Scheduled cleans will use whichever cleaning method is set as the default, so your overnight clean has used Health Check.
To change which method CCleaner uses as the default, and so for scheduled cleans, go to Otions>Settings and change the 'CCleaner Home Screen'.
Health Check has a simplified user interface, and what it cleans follows it's own cleaning rules.
The Ticking/Unticking of things (such as Firefox components) in the Custom Clean area are settings for Custom Clean only.
The Custom Clean Settings are not, and will not, be used by Health Check.
You cannot change the settings Health Check will use.</strong>
Health Check will <u>always</u> use it's own built-in cleaning rules each and every time that you run it.
Look at the Icons -
Custom Clean icon has a little 'settings' cogwheel to show you can change it's settings, - Health Check icon doesn't because you can't change it's settings.
With a manual run you can untick things after HC has analyzed, but with a scheduled clean that's not an option.
If you want more control of just what is cleaned or not by ticking/unticking the Custom Clean options then you have to use Custom Clean itself to clean.
Having said all that HC should not be removing your Firefox Bookmarks. (History yes, but not bookmarks).
I run it quite a bit for testing user issues and it has never deleted my Firefox Bookmarks.
I've just realised though that I have been aborting after the analyze and not let HC complete a clean since Firefox updated to v74.0 earlier this week.
IAs said it has been known in the past for Firefox to move where it stores bookmarks so suddenly they start getting cleaned by CCleaner. They did it in 2017.
Time for testing/investigation. (After I've backed up my current bookmarks).