I recently added a lot of files (~1100 files, 400ish MB) to a Boxcryptor folder on my Dropbox. I then realized that I hadn't turned filename encryption on.
I had a backup of everything, so I was free to experiment.
I turned on filename encryption for the folder. BC the proceeded to test it and also found an error. I had to copy the log output to a separate text file to find the error in the log - it was a filename/folder name combination that was too long. (Note to developers: please make errors in your log file stand out more!)
I then went into my Boxcryptor folder to shorten that filename and discovered that some filenames had been encrypted already (despite BC telling me it was "testing" encryption) but others hadn't.
Needless to say, that mixture of files was then unusable to me. I ended up creating a new BC folder with filename encryption enabled from the start.