OwnCloud eats files in the most insidious manner, and this is known to the devs, who in the past have suggested that the workaround is to use another sync application. DO NOT USE OWNCLOUD if you value your data!! We discovered OwnCloud eating files after about three months of office paranoia, beginning to wonder if it was an inside job of a disgruntled employee. Turns out it was an inside job of incompetent software.

Also OwnCloud DOES NOT support "delta sync" (i.e. uploading file chunks when tiny portions of files are changed, instead of, for example, needing to upload the ENTIRE gigabytes-large file when only 10KB have changed). The core devs have kicked the can down the road at every opportunity (for example take a look at the huge BountySource bug for that issue, it's like USD 1200 or something, in addition to the issue being locked to contributors because of all the +1s). This means for any use case involving large files (e.g. TrueCrypt/VeraCrypt volumes), you will quickly find yourself in a messy situation of continually uploading gigabytes of data. It was painful to experience even on a gigabit LAN.