Sub-folder setup would only require (at a minimum) one verification code located in head of the domain.com page.
This plugin puts THAT verification code on ALL pages of domain.com in a NON multi-site install.
I am unsure of its behavior in a multi-site install.
Plugin file does not exist error occurs due to the plugin file-name changing from
all-in-one-webmaster.php
to
all-in-one-webmaster-premium.php
Plugin with new file-name activates fine as you discovered.
What I noticed was that the settings data (in my case google-site-verification) was not transferred from the old version of the plugin to the new version of the plugin.
SO…..
Before you update copy all your entered data to a text file somewhere so the you can reenter it into the new version of the plugin after the update.
If like me, you have already updated, you can recover your old settings data by deactivating and deleting the new version, re-upload the old version then activate it.
The data remains orphaned in the wp_options table and it repopulates the settings fields of the old version of the plugin.
Copy all your settings data to a text file somewhere so the you can reenter it into the new version of the plugin after you update.
I had done the update on a dozen sites before I realised that all the google-site-verification fields in the new version were blank.