There are only a couple plugins (SQL & Exchange) , that use third party libraries to be installed by Core installer. As a result for these couple of plugins, since the process is running and the dlls are loaded, then those third party libraries will fail to be overwritten by the Core. Overall result, is that the plugin upgrade will fail.
This basically means that whenever you run Configure Action for SQL Server and Exchange plugins, the plugin binary will be locked forever. Upgrade will fail, and changes in the environment will affect this as well.
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