Covers are created during the menu building process. If you insert into, move to another, delete from a folder or update CBooks the cover folder will be updated accordingly (When 'Allow cover deletion/replacement' setting is enabled)
In cases you need to recreate the covers you can simply delete the cover folder and the next time the cover images will be recreated. In case all the cover images must be recreated you enable the "Rebuild covers" setting. At the end of the menus update the setting is disabled. The cover updating is synchronized with the CBook menu updating.
Tip: Don't forget to check the error reports to see if everything is gone well.