Wavelab has a batch process that allows you to add the WAV files, tell it to resample and dither to get the 16/44 files. A few clicks of the mouse and about 15 min., you have your files.
Here is my general workflow for files recorded in 24/48
1. edit in Wavelab (amplify, fades, etc.)
2. save 24/48 version of WAV file.
3. use CD Wave to track the 24/48 file, save individual tracks
4. back to Wavelab to resample/dither 24/48 tracks to 16/44 (saving to different folder than 24/48 files)
5. TLH to convert to FLAC (align on sector boundaries for 16/44 files)
6. tag files in foobar2000