[Michael Slowe] “I always understood that sticking to one codec throughout the operation is good practice.”
I agree with Michael and generally that is how I work as well. However, if your After Effects animations include an alpha channel and you render out using the Animation codec, you will end up having to use the Media 100 HD codec when importing those clips into your project (ProRes doesn’t support an alpha channel – ProRes 4444 does I believe). This will then cause a slight difference in the black levels of your finished timeline export (unless you’re dumping to tape). If there’s no alpha channel, render out of AE using ProRes and you’re good to go.
From what I’ve read, there is no discernible picture quality difference between ProRes and ProRes HQ – there is a difference in file size though. ProRes HQ only makes a difference if you’re working with real high resolution images (2K-4K) such as those from the Red camera etc. or if you’re going to be doing a LOT of image processing in AE etc. If you don’t fall into either of these categories I suggest you can stick with regular ProRes. Sounds like you’ve already started with ProRes HQ so you might as well stick with that for this project – you’re just using more storage space than necessary. Perhaps others reading can verify/dispute this?
HTH
Gary
This is me – this is what I do – https://web.mac.com/garymmw