Is there any reason why I can't export the entire database, delete all the users in Joomla/CB, and then re-import the database with generated passwords sent to each user in the email confirmation?
I suppose you could. I think CB Juice will send the emails, but I can't recall. I'd recommend testing this with 1 test user to see if it works as expected. Then do it in batches of 50 users if working ok (500 registrations at once would likely timeout or run out of memory).
Another option is to enable admin approval and random password generation within CB > Configuration > Registration. Then unapprove all of your users (ensure they're confirmed and enabled first). Now approve them and it should send them an email with their newly generated password informing them their sign up has been approved. This also works with confirmation so you can use either/or to attempt to generate passwords. As with the above suggestion test with a test user to ensure it's working as expected.