When importing one AE project into another the render queue changes

Go to the project that you want to import and delete everything inside the render queue that save it and imports it into your final project. because when you import a project you will import also the render queue of that project which can cause an issue if you don't want that queue

In English? You need to be more specific and provide exact info on your render outputs, settings, comps and so on. The default intended behavior is to append entries on the render queueu regardless of which project is imported into another, so something is specific is going on. Without any useful info nobody can tell you more than that, though.

Mylenium