Transcoding from a high data rate professional format to a more compressed format can take quite a while if the computer executing the task isn't a more powerful system.
Let us know the specs of your system (CPU, RAM, GPU) and what software your are using, and we could let you know if there is a faster way to get the job done.
If time is an issue, I would consider upgrading your storage space. It is an easy and a relatively inexpensive upgrade that would save all that transcoding time, and allow you to not loose all that wonderful image quality of ProRes.
While that is an older machine, the hour your said it took to transcode a 3 minute ProRes clip to h.264 seems too long.
I tried a test on my computer, a hackintosh with a 3.4Ghz i7 CPU and 16GB ram.
A 4 minute 1080p24 ProResHQ video transcoded in Adobe Media Encoder using its Youtube 1080p preset.
Using the the CPU for rendering, software mode, it took 4 minutes.
Using CUDA accleration, which uses my GTX 670 video card, it took 3:54.
I hope those stats help you can speed up your workflow!
RadioU TV & Animal Basement
14 years experience as a fulltime broadcast shooter, editor & broadcast designer.
Pam, which exact ProRes format are you recording to in the BMPCC? The latest firmware updates allow you to change the ProRes type. Rather than shooting ProRes HQ, try doing some tests in ProRes 422 and ProRes LT to see if the visual quality is good enough for what you're doing. If it is, then you'll save a lot of file size space that way. I wouldn't recommend ProRes Proxy as it's quite compressed. I also wouldn't suggest transcoding to H.264 to edit with, as you'll lose a ton of image data that way while adding a lot of compression. Not to mention the performance hit you'll suffer when editing with H.264 instead of ProRes.
Back in the day, we'd transcode our H.264 footage from our Canon 5D Mk II and III to ProRes for better editing, but we'd never go the other way around.