What I think you want to do with the Flickr Publish Service is let it manage all of the photos on Flickr. If you remove photos from the Publish Service and leave them on Flickr, then LR has no way of knowing that images in your catalog are associated with images on Flickr. A Collection, Publish or other, is just a catalog entry that says an image is assigned to a "bucket".
The home where you live is your address. The address of an image file is it path and folder. You might belong to a camera club, a church, and a cycling club. Yet you still live at home at your home address. An image might belong to a Flickr Collection, a Facebook Collection and a Google Picasa collection. It still lives in the folder where you imported it. Image collections are like the clubs that you might be a member of. If you want Lightroom to track your images at places like Flickr, you want to use the Publish Service. There is no reason to break that connection. If you are not using your master copy and are using your virtual copy, you don't need to keep both. You can promote your virtual copy to master by selecting the VC image and on the menu {Photo}{Set Copy as Master}
You might be called Susan at home but the people at church call you Suzi. You still live at the same home address no matter what you are called. Susan and Suzi are like virtual copies. The only time it is important to distinguish Susan from Suzi is when Susan is a brunette and Suzi is a blond (i.e. Virtual Copies having different develop parameters).