I investigates such issues some time ago: Question 1, Question 2.
In Linux, a java.io.FileDescriptor#sync call ensures that the modified data of the file associated with the descriptor is sent to the disk. (That cheap disk tend to skip the write and only place the data in an unreliable (aka no NVRAM) write cache is a different/additional problem.) It does not guarantee that also modified data of other files is written back. This is just not in the contract of sync or of the underlying fsync POSIX function.
However, in certain circumstances (e.g. ext3 in data=ordered mode), an fsync on a file writes back up modified data of the file system. This is really fun because this may create significant latencies just because some other application has created a ton of dirty blocks.