Chrome Bookmarks vanished after clearing history!
Try this to see if you're just looking in the wrong place...

Quit Chrome
Switch to Finder
Open a new Finder window,  Cmd ⌘   N 
Go To...  Cmd ⌘   Shift ⇧   G 
Copy/paste this ~/Library/Application Support/Google/Chrome/Default/ (including the tilde ~) into that Go To window
Hit Enter

What do you see?  

Bookmarks ought to be in there, along with Bookmarks.bak
Hold  Alt ⌥  &amp; drag both to the desktop, for safety.
Delete Bookmarks.
Rename Bookmarks.bak to Bookmarks
Launch Chrome

BTW, ~ (tilde) is Mac shorthand for your home folder, in My hard drive/my user name/ without needing to know what they are called. It always goes to your home folder.