What is the minimum set of files required for 3.3.0 => 3.3.1. I don't want to start from scratch. Is it admin folder + index.php? Will my sites be OK if I just replace these? Thanks,
yes
/admin
index.php
And you never have to start from scratch , you install upgrades right on top of the old install, never modify core files or themes, always make copies of them.
The entire zip is made to be extracted on top of old installs, unless you have custom htaccess rules or something nothing will be overwritten.