Excellent question!! The function of the protein can very much be affected, this is a possibility in any covalent modification of a protein, and even more so by the addition of a non natural amino acid. However one can do a variety of standard biochemical assays to probe enzyme function and if things do not appear significantly perturbed (greater than a 5% deviation from wild type rates) then we would likely suspect that the labeling is not causing a significant difference. However we would not actually know! That's one of the drawbacks to studying things this way. We have no better way to see these movements really, so it's a drawback that we have to mitigate as best we can!