We just released a new version that has a solution to the YouTube policy change. However, the solution is not a simple one.
Please review this video to see what the solution entails and why it was not a simple solution -
http://www.youtube.com/watch?v=qx12Fge81gM
mentioned in the video, YouTube will only display/return 1,004 subscription AND subscribers. Therefore, when you synchronize your Subscribers there is no way for us to get more than 1,004 (just as there is no way for you to view more than 1,004). This means, in your case, you would have to manually un-check more than 1,004 subscribers. Not very realistic but, unfortunately, there is no other way.
What YouTube really needs to do is to display all your subscriptions so you can remove them.
As the toolman mentions in our blog - YouTube still won't allow anyone to view more than 1,000 of their subscribers which limits a bunch of functionality that we'd love to add into Tube Toolbox. If anyone wants to help, you can go to the following page and click the Star (at the bottom of the page) - which is telling YouTube that you'd like to see the feature added:
http://code.google.com/p/gdata-issues/issues/detail?id=300
