My workflow is a little tedious because I am on the last leg of my old laptop, and it does not handle large files very well, so I do a lot of work on individual files them join them as a last step.
1) Create a main folder with 3 subfolders - Masters, Edits, Tracks.
2) Transfer 24/96 masters from SD722 to Masters folder, and rename each to band abbreviation plus date, plus number/letter. Example
gm2008-08-09_1A.wav, gm2008-08-09_1B.wav would be the two raw master files for Set 1.
3) Open each file in CEP and do a gain analysis on each, jotting down notes. Look at the final numbers and pick a final gain based on the numbers from each file that puts me near -1dB overall without any files clipping.
4) Apply gain to a single file at a time, with 5 second fade-ins and 5 second fade-outs on the files that represent the start and end of each set. Dither and resample to 16/44.1. Save each individual edit in the edits folder. I also create a "work file" saved in final edits that contains exact details of all post work I did.
5) Open each edited file and join them into a single file per set - dithering and downsampling does not affect seamless joins so I wait until I have the smaller 16/44.1 files to join. Save the final joined edits for each set and delete each individual edit file.
6) Track each set using CDWave, save cuesheets to edits folder, tracks to tracks folder.
7) Encode tracks to FLAC16 using FLACFRontend and delete track wav files.
Create info and ffp files and save them in tracks folder.
9) Create MD5 sum checks for each of the three folders and save them in folders.
10) Burn two sets of archive discs for the works, and verify that the archive discs all pass MD5 checksums then store.
11) If seeding to a BT site, move the tracks to an appropriately named folder, else if uploading to archive, I just use the existing tracks folder.
Sometime soon I will get a new computer that has the memory and CPU power and a newer audio software platform that can handle large files, and simplify my workflow by joining each set in 24/96. Until then, although a little tedious, the workflow I am using gets it done.