Shane is right on with his advice. Once you hit “transcode” and you get that rather draconian message that this is now a new clip and will lose all relationship to it’s camera original – that’s what you got. Don’t get me started that it could be designed to deal with that, but what are you gonna do?!?!?
So what Shane advises is the best way to go. Something to try, and no guarantees, is to transcode back in a 1080p/23.976 project, and then do a relink to selected to the correctly managed clips. There’s a chance it will work and you may only have to reword ins and outs that may have shifted due to the 23/976/25 timecode rate. In theory, it might just work. I will give it a try myself on a few clips when I get the time. Perhaps Job has tried something like this coming from the PAL world.
Michael