Hey there,
I have the same problem, using the plugin:upgrade. The plugin creates the directory "/vendor" in the dokuwiki root directory and seems to delete it after the upgrade. I know this so exactly, because I had to give write permission to dokuwiki root folder only for this action.
The dokuwiki installation is a manual installation and this time I thought instead of doing the update manual, I would use a plugin.
If uncommenting solves the problem, I'm fine with it. I also created a bug report (
https://github.com/splitbrain/dokuwiki-plugin-upgrade/issues/91)