Since WordPress 3.3, it has added a new functionality to delete the previous version of the plugin and then install the latest plugin version into the exact same location deleting in the process all the configuration folders with everything included.
In order to prevent WordPress plugin update from deleting our important folder configuration within our plugin, we must move that particular folder somewhere safe before it starts deleting everything in our plugin. After the update has completed, we will then move the folder that we want to preserved and overwrite any existing files in that folders.
This can be complex process because each hosting have different permissions and restrictions and sometimes not go well as we expect and this is the main reason that we always suggest to do a manually backup of the important configuration files in order to prevent any problem during the update.
PLEASE READ AND FOLLOW VERY CAREFULLY THE NEXT STEPS:
1. Via FTP go to the follow paths on your server and transfer a copy of the follow files and folders:
2. After the plugin update you can restore the files and folders in the same paths on your server side.
3. Is not necessary to replace the folders "0" on the configuration directory domains and agents.
We know that this process can be very annoying to do every time, but you can keep a copy of this configuration files as backup and replace any time that a new update will be made and avoid future complications.