I just performed an in-place upgrade of a very old build of FlexWiki. When I opened the site for the first time after copying in the new files, I was presented with a page asking if I wanted to upgrade the config file. I did, it brought me to admin\UpgradeConfigFile.aspx, which then gave an error saying it couldn't file <wikirootfolder>\admin\Namespacemap.xml. I'm not sure why it was looking there, as my web.config clearly stated Namespacemap.xml is in <wikirootfolder>. To resolve, I copied Namespacemap.xml to the admin folder, refreshsed the page, and the process completed saying it successfully migrated the configuration. I then had to copy the new Namespacemap.xml file in the admin folder back down to the <wikirootfolder> (overwriting the original file). Now everything works.
> So we should backup the directory as a backup before installing in
> case we need to revert?
Yes. Better safe than sorry.
> Can we just zip the entire directory and subdirectory? I assume that
> will get everything?
Yep. The only part of FlexWiki installation that isn't just a file copy is the creation of the virtual directory, and that's obviously a one-time-ever step.
Of course, this assumes that you store your .wiki files in a subdirectory of the fw install dir. This is the default (the WikiBases subdir), so unless you've changed it, you should be okay.