Some of my early EE updates (circa 2004) used the simple overwrite method. All worked well for a number of updates. Then, one day, it all went bad and nothing on the site worked after an upgrade to a new version. And, of course, since all older files were overwritten, there wasn’t a back up to go to.
Well, like I said, in my case I do make a full backup before attempting the upgrade, so when things go completely wrong and I break the site (like I did a couple days ago) all I have to do is restore the files from my backup, and I’m back in business.
That’s how I learned to build a config.php file from scratch. Still, it doesn’t take any more time to prepare a new /system directory, upload it, set permissions, and so on, than it does to upload and overwrite. It’s an up front effort that yields plenty of benefits later.
Seems like it would take a lot more time to me? I’m on EngineHosting so I don’t have to worry about permissions so I would just upload the new system directory files via FileZilla and it would only replace existing files, not replace everything (like what happened to me a couple days ago). A few minutes for the files to upload and then visit /update.php and I’m done. 😊