> It should not be surprising that given a correct assembly the bacteria reproduced - by design the experiment only replaced codons with a different equivalent codon.

I am surprised. I was under the impression that while two codons may code for an equivalent protein, bacteria do play shenanigans with DNA, like re-reading the same genome multiple times with shifted read frame. I don't think codon equivalence is preserved when you shift the read frame by 1 or 2. Moreover, a DNA molecule with changed codons is slightly different chemically at that place - which means a protein that might have previously attached there for some reason now might not.