Converting Canon 5D Mark II footage after the assembly stage

Question

I should have done my research ahead of time, but lesson learned.
I've got a 19 minute assembly of my short film completed and have already started in on the rough cut, all in the 5D's native H.264 format. The glitchiness on my MBP i7 seemed odd but I was in the zone. Finally I decided to look into it and now I've been left to figure out how to get the work I've already done preserved while I convert all my footage to ProRes 422.
I tried sending my entire bin's worth of clips through Compressor, but of course they all came out with filename's matching what I'd renamed them in the bin, so going the reconnect media route was a no go unless I wanted to do it one clip at a time, which I tried but even then I was having weird errors where the wrong clips were reconnecting - probably to do with us shooting on two cameras, and some of the file names overlapping? Hard to say exactly, but I decided to move on to a different approach.
Now I'm converting the clips straight from the finder, one camera folder at a time so as to avoid any weird overlapping/rewriting glitches since I'm making sure the original file names are preserved.
This way, when I go to reconnect media, I can point the clips from each camera to their respective folder in Finder and they will all go at once (I tested it with a small batch and it worked fine, right down to them being replaced in the sequence with the right ins and outs).
I'll post an update when the whole job is done. I'm thinking it should work out, but you never know.
If anyone has any suggestions for how this could have been done differently (apart from, you know, doing it right the first time), please feel free to share. I'm hoping this will serve as a helpful thread to anyone who, for whatever the reason, finds themselves in a similar situation.
Cheers!
Darcy

Answer 1

Thanks for this!
One minor distinction with my project is that with two cameras we wound up with two sets of clips with filenames that for the most part were duplicated, so they had to be kept in separate folders, meaning an extra couple of steps in running through Compressor and relinking in FCP so as to avoid the wrong clip relinking with the wrong footage.
The important thing is to make sure the encoded footage keeps the same filenames as the source. I'm not sure if it's necessary to move the source footage anywhere, or to put the newly encoded footage in the same folder the source footage lived in. When I relinked my footage, I simply had to choose the Locate option, which would find the original footage, then navigate to the folder where the ProRes footage lived and it grabbed onto all of it without a hitch. I had to do this for each camera's folder, which was a bit of a pain since I hadn't kept them separate in my project bin, but with a little due diligence it worked out perfectly.
Case in point, my project is now back up and running with the ProRes footage, with all my sequences preserved. Like you said, all I did for the final step was change the sequence settings to ProRes and now everything is as it should be. Footage plays back smooth, even in full screen, edits are clean and effects play back properly.
And here I was thinking my MBP i7 wasn't up to snuff. Almost feels like a new system again.
About the suggestion to go LT over HQ, I'd like to direct you to this article on the matter.
In a nutshell, the naked eye can't tell the difference, but if you had to do any keying you'd run into problems with the lower quality LT footage.
Personally, I think you should always work with the highest quality footage you can. The only real concern HQ presents over LT appears to be file size, so unless you are on some sort of super tight budget, or are working with a mountain of footage across multiple projects at once, then this shouldn't be reason enough to go LT over HQ. I have a 2TB drive dedicated solely to my short film (and a second one for backing up), so I can't see any good reason for opting for lower quality footage. Even if your naked eye can't tell the difference, you'll be kicking yourself later if you need to do something with that footage that the HQ option would have better suited towards.
Thanks again for the response!
Anyone else care to chime in?