The only way to capture HDV to ProRes is to 'Capture Now', which is not always ideal if TC is important to you.
Option # 2 it to capture HDV and convert using Compressor. It works, but is time consuming.
Option # 3 is to capture HDV, and change your render setting to ProRes. I often find this is the best solution for me since I'm using a JVC camera with a relatively short GOP which doesn't eat up a lot of resources like the Sony 15 frame GOP does. You can always bake and re-import any clips that will need a lot of filters, etc. And you can always work in a ProRes sequence too, if you like. The best idea is to try each workflow with your set-up on a small amount of material and see what works best for you.
On the make a new clip on TC break issue, it doesn't matter. HDV will always make a new clip if there is a TC or GOP break, even if you have FCP set to ignore camera start/stop. This is due to the GOP structure. One missing frame equals 6 (in JVC) or 15 (in Sony) missing frames, since they are interdependent. There is no way to ignore that many missing frames.
As someone said earlier in the thread, ProRes HQ is overkill, and gives you little in return. There are a few workflows that might benefit from it if you were doing extensive compositing , but for 99% of what most are doing, regular ProRes is fine.
Scott Sheriff
Director
http://www.sstdigitalmedia.com
"If you think it's expensive to hire a professional to do the job, wait until you hire an amateur." ---Red Adair
Where were you on 6/21?