Pretty sure it's deliberate. Back when save/load restoration was first revealed, AlexB mentioned that they wouldn't transfer between updates.
There's an obvious down side to that, but there's an up side as well: saves tend to get mucked up when transferring to new versions anyway. Even if they actually did manage to work on the whole, they'd likely be glitchy as heck.
In future, if you know there's an update coming it's best to finish up any "in progress" missions, then update.