I know this thread is sorta old, but I just ran into this while prepping all my domains for a migration. Using the DB Web Admin, issue a command like:
UPDATE `dns_zone` SET `ttl` = '300', `ttl_unit` = '60' WHERE `id` >1;
This query will change the TTL on all domains to 5 mins (300 seconds). If you need to change other things, I would recommend altering just one domain, and then looking in the DB to see what values that domain has, and mirroring it in the query. You can do this from command-line too, but I was already in the DB Web Admin when I wrote the query.
After that, run the command that Monica listed above to regenerate all the zone files.
Best of luck!