Remove operation in spring MVC

User and Checkpoint has many to many relationship. I'm able save values in database but not able to remove value from the database.

User.java

@Id
@GeneratedValue
private Integer id;
@ManyToMany
Set<Roles> roles;

@ManyToMany(fetch = FetchType.EAGER) 
List<Checkpoints> checkpoints;

public User() {
    super();
}

public Integer getId() {
    return id;
}

public void setId(Integer id) {
    this.id = id;
}

public List<Checkpoints> getCheckpoints() {
    return checkpoints;
}

public void setCheckpoints(List<Checkpoints> checkpoints) {
    this.checkpoints = checkpoints;
}

Checkpoints.java

@Entity
@Table(name = "checkpoints")
public class Checkpoints {

@Id
@GeneratedValue
private Integer id;
private String description;

@ManyToMany(mappedBy = "checkpoints")
List<User> user;

public Checkpoints(){

}
public Integer getId() {
    return id;
}
public void setId(Integer id) {
    this.id = id;
}
public List<User> getUser() {
    return user;
}
public void setUser(List<User> user) {
    this.user = user;
}   
}

In controller adding checkpoints works fine but after removing checkpoint object from user when i save user, it doesn't save in database. UserController.java

@RequestMapping(value="/checkpointadd.html", method = RequestMethod.POST) 
public void checkpoint(@RequestParam Integer categoryId, HttpSession    session){    // This works fine
    System.out.println("Checkpoint checked :"+categoryId); 
    User user = (User) session.getAttribute("loggeduser");
    Checkpoints cp = userDao.getCheckpointById(categoryId);
    user.getCheckpoints().add(cp);
    userDao.saveUser(user);
    user.getCheckpoints().remove(cp);
}

@RequestMapping(value="/checkpointremove.html", method = RequestMethod.POST) 
public void checkpointremove(@RequestParam Integer categoryId, HttpSession session){   // I'm doing something wrong here
    System.out.println("Checkpoint removed :"+categoryId); 
    User user = (User) session.getAttribute("loggeduser");
    Checkpoints cp = userDao.getCheckpointById(categoryId);
    user.getCheckpoints().remove(cp);
    userDao.saveUser(user);
}

In my UserDaoImpl

@Transactional 
@Override
public User saveUser(User user) {
    // TODO Auto-generated method stub 
    return entityManager.merge(user);
}

Please let me know what i'm doing wrong or other approach to do the same!! Thanks in advance!!