Hi Shaun, if I understand correctly you are right clicking items in your 'recent uploads' and choosing to delete them, that is why you are getting the warning as items deleted from the recent uploads (read core library) are removed from your storage quota. If you are deleting iterations of an asset from your library folder structure then you won't see that message as these are 'copies' of the original (but don't count against your quota, simply to allow the same image to exist in multiple folders for organisational purposes).
If I'm not quite getting it right please supply screen shots, the long and short of it is that nothing will be removed from your library without you removing it yourself?