I implemented the following in the repository for that class and it seems to work well (in a couple of tests I've tried):

public void Update(SChannels entity, List<ScsgLink> deletedLinks)
        {
            try
            {
                EntityState entityState = _siriusContext.GetEntityState(entity);
                if (entityState == EntityState.Detached)
                {
                    _dbSet.Attach(entity);
                    _siriusContext.SetModified(entity);
                    foreach(ScsgLink link in deletedLinks)
                    {
                        _siriusContext.SetDeleted(link);
                    }

                    foreach(ScsgLink link in entity.ScsgLink.Where(s=>s.Added==true))
                    {
                        _siriusContext.SetAdd(link);
                    }
                }

                SaveChanges();
            }
            //catch (DbEntityValidationException dbex)
            //{
            //    var msg = dbex.EntityValidationErrors.ToList();
            //}
            catch (DbUpdateException ex)
            {
                ThrowError(ex);
            }           
        }

I had to add a new NotMapped Added property and a DeletedLinks to the ViewModel and make all necessary changes. So, this is not generic enough, but I'm not sure how to make the above more generic.