Creating an artifical bacterial genome and transplanting it into a bacterium is still a huge effort and far from routine. As far as I know it has only been done

Creating an artifical bacterial genome and transplanting it into a bacterium is still a huge effort and far from routine. As far as I know it has only been done once, and it did cost some tens of millions of dollars. Genetic manipulation is typically done at a much smaller scale, and not by exchanging an entire genome. And on a small scale it would be very unlikely that such a switch would go unnoticed. The way back from bacterium to executable is also extremely unlikely, there would be enough mutations after some generations that the program is unlikely to run at all.