I've been typing the same question in search engines finding people with the exact same question as me but with no answers. This has wasted me hours of game time for no purpose.
I completeled all the liberation missions in east New York but my contact has dissapeared and when I go back into the same bar where I met him I see the liberation symbol in the bar but he isn't there.
I think I know why this bug happened though, because I think I screwed myself from completing the west New York liberation too. I talked to both of the contacts like it tells you to do before I completed all of the other parts of the missions for both east/ west. When I was in the west and talked to the doctor a second time he b*tched me out and told me not to come back until I brought more typhus ridden people there and then he dissappeared off the map along with any other liberation symbols. I just accidently walked to the typhus ridden mats that weren't on the map and got an option to burn them and it checked another part off the list for west new york liberation.
Besides that I've noticed that it's funny that I was just in valley forge where it says the American army is there to protect congress in new york from British occupied Philadelphia yet New York is occupied by the british as well!
Another glitch in British New York (I just completed sequence 9) is that even if I'm incognito sometimes I still get recognized and chased around for no reason.
So I guess there's no point in playing the side missions at all. I really wanted to use a fleet of ships for trading and craft a dual pistol holder along with recruiting more than the 2 allies I have now, which I won't be able to do because they both dissapeared! lol
They should have really removed the auto save function from the game and let us save our own files for this exact reason! So I guess I'm just going to be playing the main game instead of wasting time on the extra side missions.... >:-/
Every liberation mission is still out there, waiting until you complete it. It's just that the marker may not be showing, meaning you have to manually hunt it down. Use the maps on the FAQ page for help with that.
I had this exact problem in Boston. Just got to find them.