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I have messed things up in the past so I am going to ask first just to make sure . . . the directions for upgrading (I am going from 1.6.3 to 1.6.4) tell me to move all of the downloaded files into the directory where I currently have MyBB (sans that settings.php file). But the directions are very brief so I do not know whether I am supposed to move the new files 1 by 1 to where they belong or just FTP all of them into the main directory at once, etc. I am worried that I will replace the current files and screw something up OR that I will merge the new with the old and screw something up. Can someone tell me whether to replace or merge or even if I am supposed to copy the top level files over and then open each folder and individually copy the contents over? Thanks for these additional helpful directions.
You are supposed to upload the files to the root of your MyBB installation (i.e. where the index.php, member.php or search.php files are). You must overwrite (or replace, as you call it) all the old files with the new ones.
FTP all of them into the main directory at once !
I worry about things like the uploads folder I am uploading (along with everything else) replacing my current upload folder that contains many user avatars. Ah well, here goes nothing. ;~)

And thanks in advance.
^ that upload folder will not be changed !!
You'll be fine, don't worry. The upgrade script is pretty straight forward, and it wouldn't remove your avatars at all (nor would the file uploading delete it).
Well, apparently it didn't want to go smoothly. I'll figure out what I did wrong. I did remove the settings.php from the inc directory before uploading everything else. And, on the server I can see the install/upgrade.php file so I am not sure why it's not finding it. Hmmm.

Warning: require_once(/home1/jayhawks/public_html/jayhawk/mybb/inc/config.php) [function.require-once]: failed to open stream: No such file or directory in /home1/jayhawks/public_html/jayhawk/mybb/install/upgrade.php on line 41

Fatal error: require_once() [function.require]: Failed opening required '/home1/jayhawks/public_html/jayhawk/mybb/inc/config.php' (include_path='.:/usr/lib64/php:/usr/lib/php:/usr/share/pear') in /home1/jayhawks/public_html/jayhawk/mybb/install/upgrade.php on line 41
It's not the upgrade.php file that's missing, it's ./inc/config.php.
Ah yeah. I notice in the directory I uploaded that there is no ./inc/config.php -- it's config.default.php -- should I rename it it work?

I am on a business trip on my laptop, but I do have the original files backed up on my computer at home. I am not teaching until early Sept. so this isn't urgent and I can wait and add the former config.php file early next week if that's what is needed. Thanks for the help and responses.
And, I am also missing my avatars and stuff. I fear I was not clear about replace and merge. I will have to wait until I am home to upload the files that have been overwritten, it appears. This is the same thing that happened to me the last time I did a simple upgrade so I am apparently using my FTP program incorrectly (Transmit on a Mac).
This is what screen I get and I clicked "Apply to all" and then "Replace" and it always seems to overwrite everything. I probably need to be more clear in asking my questions here, too. Undecided

[attachment=23780]
Fwiw, I just remembered I can use my cpanel to restore a directory so I am right back where I started and everything looks just like it did at 3:00 AM earlier today. Whew!

But I think I'll wait to upgrade until I figure out what I am doing wrong. Heh.
Your FTP client seems to be misconfigured. What it' should do is leave existing files on the server if they're not in the set of files you're uploading, but yours isn't doing this.

For example, config.php isn't in the ./inc/ folder by default. When you upload the inc folder, it should just leave the config.php file that's already uploaded, but it's not, it's replacing the whole of the inc folder with exactly what you're uploading. It shouldn't do this, and it's not something you're doing wrong or a problem with MyBB, it's how your FTP client is uploading the files. Unless you try the Merge option, that might be it.
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