Plugins disappear from all sites and network admin after deactivation

I just updated WP to 4.6. After, I decided to update some of the plugins. I’m running a multisite network.

In the network admin, there is an “update now” option beneath each’s plugin’s Edit and Deactivate buttons.

I pressed “update now” and received an error message. I deactivated the plugin and it disappeared from the plugin list.

Then when I FTP and try to access the folder, I get an access denied message from my server, even though I was able to access the specific plugin folder via FTP before I tried to update it.

If I wait a few hours and FTP back into my plugin folder, the folder for the specific plugin has been deleted off the server. I can reinstall the plugin and it works fine. Here are my questions:

1) Should I deactivate a plugin before I update it?
2) Why does WP 4.6 delete a plugin when I deactivate it?
2a) Is this a bug in 4.6.

Thanks!