Deleting the pl_id_mapper file will make the plugin to reregister to Site24x7 server. In most cases, it will not affect the plugin. But when there are multiple plugin versions available in the account across different servers, and the plugin version of the current plugin is less than the higher version of plugin available, it will not register and will ask you to increment the plugin version for the data collection to happen.
If you don't want to face that case, please remove only the key and the value object for the plugin you need to remove. And make sure you don't change anything else in that file.
After the agent restart, only the available plugins will be sent to client. Hope this helps. Let us know for further queries, if any, in the below thread.