To be extra secure while syncing data with OwnCloud, I put some confidential data into a TrueCrypt container. However, the container wasn’t synchronized by OwnCloud’s Windows client after I changed the data inside the container.
I quickly found out that the problem was TrueCrypt not updating the modification date of the container (which is a nice security feature of course). OwnCloud simply didn’t realize that the container had been changed. However, there’s a configuration switch that disables this feature:
Settings -> Preferences -> Preserve modification timestamp of file containers
After unchecking the setting OwnCloud now syncs the TrueCrypt container just fine.