I asked the FTM techs this same question and obviously there is no way to synchronize FTM 2009 with online trees. The thing that bothers me the most is that when you upload from FTM 2009 to Ancestry.com, then invite people to add to your family tree, your invitees will be deleted when you upload again whether you delete your old tree or not.
You would think that the same company who owns
Family Tree Maker and Ancestry.com would make the two work together rather than concentrate more on their online family trees which I'm sure are designed to make more money for them because your sources link to their sources requiring others to subscribe.
Don't get me wrong. I love FTM 2009, but I think the online tree (which I use for sharing with family) needs major work. I also think that we should have more control within FTM 2009 as to what we want to upload.