How do I convert all custom_field php timestamps in the database to js timestamps?

ACF using milliseconds is not standard for timestamps, and nor is it useful.

How much accuracy do you need? Bear in mind that converting to something like yyyymmdd will not accommodate timezones.

If you have access to PHPMyAdmin (or similar) and know your way around SQL, running a quick query would probably be the easiest solution, although ACF’s milliseconds would annoy me so much I’d reconsider using that plugin.