Sorry about that! Do you have a link to the repository you were trying to run? Maybe there is something we can tweak.
When your kernel is not busy for more then ten minutes we stop it (save the notebook and restart the kernel). If for ten minutes or more no kernel is running we remove the whole binder (your work is lost). Unfortunately there is not much you can do about this beyond not letting your kernel stop running (which is tricky in a teaching situation).
We are thinking about and trying out ideas for how to make it possible for people to recover their work or even start a new binder from one that used to exist (but has expired). It is a bit tricky though 
Overall the reason we are so aggressive on removing “inactive” instances is that mybinder.org is a free resource so our budget for compute power is limited 
Today (about 8hrs ago) and about 4 weeks ago we did some maintenance which could have interrupted things more than usual, though you would have had to be active in a particular five minute window.