The next version of Necken will include a feature requested multiple times: A save system!
While the 0.17.0 version is not completed just yet, there's an updated version in the [Development] branch available, if you wish to try out the new save system right away!
It should be working fully, and I'm releasing it early since I haven't found any bugs with the new system.
So, if you're interested in testing the new save system before everyone else, make sure to switch to the [Development] branch in Properties > Betas.
More info about switching branches in the FAQ post in the forum.
Cheers,
Joccish