I had this problem a week or so ago, where changes made on my ToodleDo web weren't syncing with my iPhone. Now I'm getting the same error, one minute it was OK and now it's not syncing. I haven't changed any settings.
Last time I forced a one-way web to iPhone sync which got everything synced, and it was OK after that. I shall have to do the same thing now but am concerned that this keeps happening - it's made me paranoid about random checking after every update.
I am sorry that this has happened to you. There may be a bug with auto-sync that is causing this when there are poor network conditions. You may try switching to manual sync. We are looking into the problem.