Got an answer today from one of the ownCloud developpers. It’s quite simple but disappointing…
The ownCloud file “cache” stores encryption counter for your files. Without a proper counter, no file can ever be decrypted and your data are inaccessible, either from the web UI or through sync to another computer.
Consequence is you should never flush the file “cache” if you use encryption and, at large, it seems that you should never flush the cache at all…