me too
make sure to use quick cluster.
What do you mean by "Quick cluster"?
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I had that problem too and no handy solution yet. My Experiences:
*MediaManager in FCP often stops/hangs way too often on some clips, aborting the whole Process (while i am away, thinking it's transcoding) instead of just ignoring/skipping bad files and make a Proper Protocol about them. Sorry, but It's crap.
*Compressor is slow (not so much the encoding itself, but the GUI is soooooooo slow) or crashed at huge batches.
*Adobe Mediaencoder crashes at huge batches. TC Support unknown.
Red Giant Software does a App for this, but they don't say anything about Timecode.
*Sorenson Squeeze, not the fastest Kid too (i mean the Interface) but more stable than Compressor in my experiences , TC not tested but anyway too expensive for my needs
*After Effects, it may preserve the TC If QT is not added to a new comp, but doing rightclick at the Clips "make proxy" or "add to renderlist" directly (make shure to set the default export modules for "Proxys"/"add to render list" to your needs)
I did something different:
I did the conversion in Streamclip and then afterwards added the original TC with the tool "QTChange" from Videotoolshed. The developer is very supportive and fixed/added features within a day for me. While it worked for me, the method isn't 100% reliable, since QTChange is originally designed to apply TC out of the either Canon .THM Files (very cool Feature!) or by Timestamp (Time written) of the QT File. Its ALE-I/O-Feature I (kind of miss-)used was originally to transfer logged Files/Projects from Avid to Finalcut Pro.
So my workflow whas as follows:
1. scan/load the directory with the Originals QTs (those with TC) and export an ALE out of QTChange. (an ALE out of Avid or Metacheater should do also)
2. scan (load) the Directory that contains the Proxy(Offline) QTs (without TC)
3. select "use .ale", you see the list updating to a preview of the changes
4. apply changes
Problem was that at some files the app coul'nt delete/add the TC Tracks. But after a few repetitions it worked.
But that's a not a very comfortable way and also there is still the Problem that MPEGStreamclip does always reencode the Audio to either 1-Track-Stereo or 1-Track-Mono 16bit integer. (There is no Audio passtrough) Which always differs from my original media in FCP and it seems, that FCP is always having hickups and Problems when some Tracks in the Proxys are missing or different flagged to the original Clips. In my Experience.
But, maybe Compressor is still the best way to go: possibly when generating and using a Droplet instead of adding files and presets to the batchlist manually. I forgot that possibility. This could be worth a try. You can also setup network render via qmaster to improve render speeds, but when i look at your 4444ProRes, i guess HDD/Network Troughput is your bottleneck, not CPU Power alone.
HTH, hauke