For HDSLR transcodes I always use MPEG Streamclip. It’s free, fast, and maintains the original file name.
Here’s a good way to do it. Create an identical folder structure to the one you are currently using, but use a different name for the root folder. Create a batch in MPEG Streamclip, and select the h264 footage (one folder at a time, choosing the new identical folders as the destination). Start batch and wait.
When it is done, quit out of FCP, change the name of the root folder for the new transcoded footage to the name that the h264 footage folder uses.
Re-open FCP and the files will be re-linked automatically. Done.
You’ll probably have to change your sequence settings, but shouldn’t need to render anything (unless you used effects).