See: https://www.phplist.org/manual/books/phplist-manual/page/upgrading-a-manual-installation

Overview If you installed phpList manually, this is the correct installation method for you. The process consists of the following steps:

• Unordered List ItemDownload the archive containing the new version to your server (e.g. to your home directory)
• Decompress the files
• Back-up your database using your preferred method (e.g. using Mysqldump)
• Copy (Back-up) your config.php file
• Remove your old `lists` directory and replace it with the new one (actually, you should overwrite all files, directories and sub-directories from the 'lists' directory top level path and downward. This will preserve any custom-added subdirectories, like 'uploaded-attachments'
• Copy your backed-up `config.php` file over the freshly uploaded 'config.php' file in the new `lists/config/` folder
• Login to the phpList admin interface and automatically upgrade the database following the prompt