It depends on how good you are at multitasking. You don't want to neglect your advisor's projects because you're working on a side project. At the same time, you don't want to neglect your side project because you're working on your advisor's projects. (Your collaborators will probably be happier parting with you on good terms than collaborating with you on a project that you'll never actually work on.)
Keep in mind that you'll also have other side projects with more urgent and demanding deadlines, like classes or being a teaching assistant. As a PhD student my attention is normally split between two or three tasks, even without external side projects.
If you want to continue your side project, you should definitely ask your advisor if you can keep working on it, so he knows about all your commitments (and is okay with them). You might even be able to pull your advisor in as a collaborator, and then everyone's happy!