Hi Hal,
Not sure if you have figured this out yet, but just to let you know, handbrake should be able to handle prores just fine. I do this all the time without a problem. If not, that means you need to download some additional codecs from Apple's site, or, do a software update (once you install the Final Cut Suite, Apple's software update should realize this and download the "pro" codecs for you. These are playback codecs (obviously, since you can use prores inside FCP already), and get hooked into the general quicktime framework, which I think handbrake leverages. Though if not, you should be able to find them for download by looking at the support area for Final Cut Pro).
Another alternative is to use compressor to create the final output file.
One thing you shouldn't do (for your final release at least) is do two encodes (one through compressor, another through handbrake). It should be ok for a workprint, but you want to limit the number of encodes you do due to quality loss that each encode will introduce. Granted, going from prores to prores won't really do much to the quality...but it is strange that your version of handbrake won't let you use the native prores. Make sure you are using the latest release of handbrake. (no need for beta versions, latest supported release should be fine).
Not sure if you have figured this out yet, but just to let you know, handbrake should be able to handle prores just fine. I do this all the time without a problem. If not, that means you need to download some additional codecs from Apple's site, or, do a software update (once you install the Final Cut Suite, Apple's software update should realize this and download the "pro" codecs for you. These are playback codecs (obviously, since you can use prores inside FCP already), and get hooked into the general quicktime framework, which I think handbrake leverages. Though if not, you should be able to find them for download by looking at the support area for Final Cut Pro).
Another alternative is to use compressor to create the final output file.
One thing you shouldn't do (for your final release at least) is do two encodes (one through compressor, another through handbrake). It should be ok for a workprint, but you want to limit the number of encodes you do due to quality loss that each encode will introduce. Granted, going from prores to prores won't really do much to the quality...but it is strange that your version of handbrake won't let you use the native prores. Make sure you are using the latest release of handbrake. (no need for beta versions, latest supported release should be fine).