This is very bad indeed. First of all, please update to 2.1. 1444 (if that in fact was not what do have).
I’m not quite sure what happened here. You’re saying that you renamed a file within the decrypted zip, and then “all the files disappeared” – from where? The zip?
I’ll have to try to recreate this. Follow the progress here: https://bitbucket.org/axantum/axcrypt-net/issues/189/zip-file-emptied-during-rename-of .