I'm facing the same issue on the second website. Everytime I update a plugin, this disappears from the plugins directory and its files completely overwrite those in the active child theme directory.
At a first glance, on the first website, I thought this behavior was dued by a server misconfiguration because it happened only on a website hosted on an Azure environment set up by my own company, but today I encountered the same issue on a website hosted on a managed Cloudways server.
This behavior on the second webiste started after updating to the latest WP version. Both of the websites are based on custom main and child themes.
Do you have any advice to point me in the right direction on how to solve the issue?