The idea for the experiment was to see if the pastry could still be eaten once it had returned to Earth as it would have been exposed to -36°C.
Since the balloon and the pastry were lost it is sadly now impossible for the students to conduct this side of the experiment.
Speaking to BBC News, Liz Scott, who is the director of studies at the school was still hopeful that the Bakewell tart will turn up, somewhere:
Last year, we launched a high-altitude balloon in preparation for this experiment and it was found by a couple on a beach near Skegness, who used the contact details on the balloon to let us know where it ended up.
We're hoping the same thing will happen again and we'll find out where the pudding ends up.
£1,600 has been raised by the school for Guide Dogs for the Blind as the experiment was sponsored by local firms.