Generally speaking, you need to update all the files from the release. However, the .htaccess file does not change often, so may not need updating. You could keep an unmodified copy of files you have used and compare them to the build. Anything that has changed in this comparrison you would need to deal with.

zp-config.php is not included in the build, it is generated when you first run setup.php. So you do not change it when you install the nightly build.

Aaaah~~~ IC...thank you very much.