assuming there's no backup... just a few ideas...
Maybe you have another machine that did not run BoxCryptor before?
If yes, I'd try and install the older version - if files accessible, BACKUP them. If not, I'd try the latest version, maybe that helps...
Do you have a backup that could set the machine at a state BEFORE the upgrade of Boxcryptor? (In that case, you'll likely want to backup the latest state?)
What happens when accessing the files without Boxcryptor, I mean directly, e. g. via Website or so?
May I ask who your webspace provider is?