I know what you're thinking: "You have to sync the audio first, then edit later! gahh!"
Well, this may be true, but imho, there definitely SHOULD be a way to do this, particularly as an AE who can save a full day of trimming work by doing it while sitting around on set, doing nothing.
One workaround is:
1. Edit the raw files
2. At the end of the day, get the audio. Attach synced audio to the dailies and export exactly full length, same name transcodes of dailies
3. Offline the files in your edit, and reconnect them to the transcodes
Voila, synced audio on your edit.
There are problems with this though, and I won't bother naming all of them. One obvious one is that you might make a tiny error somewhere making each transcode video. Another is that you now have another huge pile of video data to have to move around and deal with. Basically, it would definitely be more manageable to edit merged clips rather than transcodes.
That being said- i REALLY wish there was a way to take the edits performed on a video clip and simply apply the exact same edits to a merged clip of the same length. I was trying to get into scripting to try to sort this out, but I figured I'd ask here first. It looks like the scripting support for Premiere is nonexistant, although you actually can script for it anyway. Any thoughts?
To keep your original clipping, dupe sequence. Save project.
Get clips merged in Prelude, send to premiere pro, import other project, go to project panel, open dupe sequence, in project panel, select prelude timeline (do not open), go to dupe sequence, right click edits, and replace each "clip" or edit section with the one from the panel.
Alternatively, take your original video, create sequence, nest that sequence. Edit the nested sequence. Replace the video in the original sequence with your merged clips and render out previews, then do the same for your nest.