I had a similarly annoying experience, but with Dropbox. On my Ubuntu PC, I created an encrypted folder in my Dropbox using EncFS. Turns out EncFS produces ver

I had a similarly annoying experience, but with Dropbox. On my Ubuntu PC, I created an encrypted folder in my Dropbox using EncFS. Turns out EncFS produces very long folder names and file names if you use the default, most secure setting with per-file IVs. Still, everything worked fine until I booted my Windows PC. As soon as Dropbox started trying to sync with the Windows PC, it ran into the 260-char path length limit and quietly began to truncate their names. Result: corrupted EncFS folder.