Sorry for the late reply, I missed this thread.
Auto-bind was used to bind Eclipse projects to specific modules in SonarQube. The concept of modules has been dropped from SonarQube, so now you “just” have to bind all your Eclipse projects to the same SonarQube project. This is of course assuming they are modules of the same project.
If you want to bind multiple Eclipse projects to different SonarQube projects then indeed the situation is a bit more difficult, especially if you have many projects.
We are discussing bringing back auto-bind at project level, but this is a complex topic to do it right, so no short-term plans.