Can you maybe elaborate a little on how you are creating the new project, and how do you "install" your plugin to said new project? The behavior you are describing sounds like either the entire project is getting copied, in stead of just the plugin, or the plugin contains content, and when the plugin is copied over, it will obviously bring in any content contained within that plugin.
If you then make changes to the plugin content from your project, and creating a new project, then copying the plugin to this new project, from your previous project it will of course include any changes you made to that plugin content.
What you need to do is have the plugin exist somewhere outside of your projects, and only copy from that location, then have your projects modify the plugin content as they need to
Or even better, use source control and put your plugin in source control, and get it from there, then if you need to make changes that are project specific, duplicate or extend the plugin content to a location inside your specific project only, then modify that content without changing the plugin
any changes to the plugin will then be detected via source control, and you can decide what you want to keep/discard, what needs to move or get merged etc.