Flushing only file metadata

I am a newbie to FS. But when you go through implementation of any physical FS (ext4/ext3/etc) they haven't exposed such functionality to upper layer. But internally in fsyc() implementation they only update metadata of the file and remaining task is delegated to generic_block_fdatasync(). You might want to write a hack for your requirement of flushing only metadata.

Anyone know of a way of only flushing the file metadata?

No, Based on my understanding, there is no interface/API provided by any operating system. There are two types of the interfaces provided by FileSystem through which application(User mode) program can control when data gets written/saved to disk.

fsync: A call to fsync( ) ensures that all dirty data associated with the file mapped by the file descriptor fd is written back to disk. This call writes back both data and metadata.

fdatasync: This system call does the same thing as fsync( ), except that it only flushes data.

This means there is a way to perform something opposite to the task mentioned in this question. However while reading your question,it appears to me that you want to achieve this to get optimal performance and data consistency. With my understanding we should not think much about the execution performance as modern FileSystem implements the "delayed write" and various other mechanism to avoid unnecessary disk writes.

The main intention over here is to switch between User Mode and Kernel Mode as it is more expensive compared to anything else. This might be reason that kernel developer has not provided such interface which can only be used to update the meta data of that particular file. This could be due to limitation of the FileSystem and I guess here we can do little to achieve more efficiency.

For complete information on internal algorithm you may want to refer the great great classic book "The Design Of UNIX Operating System" By Maurice J Bach which describes these concepts and the implementation in detailed way.