plugin in root

This is the root website on our server with several additional domains on the cpanel. We found the security changes this plugin did to the htacess files are being applied to every site below within the folders. Example of the subsites exampleb.com the readme.html file is being redirected even though the plugin is not installed.

To make is worse then there was some caching scripts applied to the root htacess file that was then applied to all subsites. So we had a plugin conflict on one site.

Is there a setting to not have this happen? We did call hosting and confirm this should not be happening and it was coming from the plugin. We also are using php 7.4 on this server.

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