Yes, by all means, make backups of the directories you will manually remove.
Just to be clear .... please verify ... the *contents* of moodledata/cache/ and moodledata/localcache/ were the directories recommended to remove.
And yes, those will rebuild as one clicks around Moodle ... IF ownerships/permissions allow Moodle to re-create them and write to them.
'spirit of sharing', Ken