Optimizing bulk update performance in Postgresql with dependencies
Given that you can not afford to drop and recreate the table, this related answer would be a better fit:


Best way to populate a new column in a large table?


You might drop expendable indexes and recreate them when you are done (if they aren't completely expendable).

And all the general advice for performance optimization applies.

There is not much more you can do, if you have to update the table bit by bit. Faster alternatives drop and rewrite / recreate from scratch.