To update a ZIP file, the file has to be opened with ZipArchiveMode.Update instead.

using (FileStream fs = new FileStream("archive.zip", FileMode.Open))
using (ZipArchive archive = new ZipArchive(fs, ZipArchiveMode.Update))
{
    // Add file to root
    archive.CreateEntryFromFile("test.txt", "test.txt");

    // Add file to subfolder
    archive.CreateEntryFromFile("test.txt", "symbols/test.txt");
}

There is also the option to write directly to a file within the archive:

var entry = archive.CreateEntry("createentry.txt");
using(var writer = new StreamWriter(entry.Open()))
{
    writer.WriteLine("Test line");
}