Thanks guys for the responses. The first try cutting out the extra import step worked fine and cut down a good deal on time, but my next question is about this, page:
Mix/Render as 44.1 prior to export and then export. There is something about the resample during export that doesn't seem to keep the label positions correct, I've had it happen the few times I was doing resampling.
The problem for me (but I haven't experimented much) is tracking (in audacity terms, "labeling"). I'd like to import the original recorded files (24/48), mix, then set down track labels, then export both 24/48 and 16/44 versions, but I can't seem to be able to change the sample rate on whole track and keep the labels where they should be.
However, I thought about the unusual export process and did this per the advice given:
I started with the 24/48 track, set down label markers for each song (tracked), export to flac 24. No problem. Then I changed the "project rate" as a whole (in the bottom left corner v. 1.3.14), to 44.1, but didn't change it on the actual track itself, so the track is still labeled 48000 and the change in project rate hasn't shown up. I assumed due the weird export rules of Audacity that would do the trick so when I exported to flac 16 it would be at 44.1 even though I hadn't changed the actual track itself. Apparently it worked. I fixed the SBE in xACT with no "this is not CD quality" errors (as opposed to when I had in the past tried it with 16/48).
I really hope thats all it takes, but page are you saying sometimes when doing that Audacity won't resample the export with the label markers where they should be? I decoded them back to .wav and put them in itunes and they're tracked out as they should be.
edit: I'm using the word "track" to talk about two different things.