gistfile1.py

from sqlalchemy import Column, Integer, ForeignKey
from sqlalchemy.orm import relationship
from sqlalchemy.ext.declarative import declarative_base

Base = declarative_base()

class Link(Base):
    __tablename__ = 'Link'
    id = Column(Integer, primary_key=True)
    doc_id = Column(Integer, ForeignKey('Doc.id'), nullable=False)
    order = Column(Integer, nullable=False, default=0)
    def __repr__(self):
        return 'Link(id={})'.format(self.id)

class Doc(Base):
    __tablename__ = 'Doc'
    id = Column(Integer, primary_key=True, autoincrement=True)
    links = relationship(Link, order_by=[Link.order])

a2 = Link(id=2)
doc = Doc()
doc.links = [Link(id=1), a2]
old_links = doc.links
print old_links # [Link(id=1), Link(id=2)]

doc.links = [Link(id=3), a2]
print old_links # [Link(id=2)]