[ffooky]

You can definitely do it with Audacity but whether it's the best tool for such a conversion I really don't know.
I'd take a punt that QT might do the job better and I'd go about it like this:

1) Make a cue file of the original 48kHz FLAC's with xACT.
2) Join 'em all up with xACT.
3) Export the resultant big FLAC to 44.1kHz AIFF with Toast (Best Quality render setting, 16 bits sample size).
4) Split the big AIFF according to the cue file you made in 1) which will guarantee sector boundary compliance.
5) Toast the buggers.