In order to create a synthetic bacteria, a new chromosome must be produced. This is done by synthesising oligonucleotides, and then ligating these together to form a complete chromosome, containing the intended genes. This final chromosomal construct is propagated in yeast before transplantation to a host bacterium.
This chromosome is then inserted into a host bacterium, along with restriction enzymes. These enzymes degrade the existing chromosome within the bacterium, preventing it from being used by the bacterium.
This is a good way to carry out large modifications to the bacterial genome, allowing easy genetic manipulation (including knockouts, knock-ins, …).