PDB said:
So I guess we get back to the heart of the matter, is it worth all the trouble to convert to 48? Does changing it to 48 affect the quality?

It inevitably affects quality. The high-quality resamplers minimise the damage.

Converting to 48 is unavoidable if one must have a disc playable in a stand-alone player, which is an understandable requirement; however, if it's done after editing, two tracks can be released: one at 44.1 and one at 48. This way, nobody loses: those who wish to remux to MKV have the option of keeping the original sampling rate; those who want a resampled version can have it; the only change in the editor's workflow is that he resamples the guide track, rather than the track that he wishes to sync.

Again, I'm sincerely sorry if it looks like I'm pushing to have things my way, but it doesn't make sense to me to insist (justifiably) on bit-perfect rips and then to resample the result, especially in a less-than-ideal way. It's a bit like insisting on buying paper of the highest quality and then giving it to a two-year-old to doodle on it (though obviously that analogy's an extreme one).