I wrote an applescript that automates the process of converting 16/44.1 flac, first to 24/44.1, and then to 24/96, using a combination of 'Sample Manager', 'Max', 'Flac Tools for OSX', and 'Steel Bank Common Lisp'. All of this software is free, except for Sample Manager, which uses the same SRC as Wave Editor, and it costs about the same as well. Sample Manager is intended more for automation of rather simple processing routines (e.g., what we're trying to do here), whereas Wave Editor has a much larger set of processing tools available but can't be automated nearly as easily.
My applescript works by keeping a 'source' directory synched with a 'destination' directory, where all 16/44.1 flac files in the source directory will have a 24/96 processed flac copy in the destination directory. Tag information is moved to the processed flac file as well.
If anyone is interested in getting a copy of this code, send me an email, and I'll take the time to polish it...