Firefox stores informations about how often you choose a bookmark using Awesome Bar dropdown. Then you have just to type one or two letter and your favourite bookmark will be opened without the need to find it manually. Recently CCleaner started deleting the file that contains informations about how often you choose bookmarks. I noticed that with disabled history clean everything is being kept. I'm unable to use CCleaner with history cleaning so my suggestion is to make another option especially for deleting Awesome Bar history which I could leave "unticked".
If they're stored in separate files you may want to try this:
Place an exclude on the file you want to keep by starting CCleaner then click Options, Exclude, Add File.