That's the same as in Android. If you check "encrypt filename" and next time uncheck it and each time save any file then
you get it two times, one with filename encrypted and one with not encrypted filename.
Maybe the programmers can display a warning or can prevent from creating two files with same name.
You can see, that these are two different files with different filenames, if you open OneDrive or Dropbox account
directly without Boxcryptor.