I am trying to confirm this, but I suspect plugin upgrades generally recursively delete the existing plugin folder and installs the new version fresh. ie there should only be core code in a plugin folder.
Unfortunately, WP-o-matic stored its cache under the plugin folder and that has been lost due to the upgrade.
I have no connection to the plugin author but I will share my recovery experience to assist anyone finding the same problem.
First thing to realise is that the files have gone from your system. There is not a quick fix to restore them.
To recover from this loss, you will need to recover from a backup if you have one. This folder only “/wp-content/plugins/wp-o-matic/cache/”.
Rename the existing folder first, you do not want to lost any files since the upgrade. Merge these back into the recovered folder.
You will still be missing files between the backup date and the upgrade date. I personally lost files between 8th Apr and 10th May. Grrr.
It is a long time since I configured WP-o-matic, but I am sure it will be possible to tell it to reload articles. I will let you know what I find.