I have lived on the same place for about 20 years, and most of my flower gardens have been made by transplanting. For many kinds of plants and flowers, it is very healthy to divide and transplant them, and this continues to give me more garden area to work with.
When I am transplanting something and pruning the roots, I make sure to keep the equipment for that separate. I also clean the equipment well throughout the year.
It is much healthier for your plants when your equipment is clean and you also minimize the risk of transferring certain diseases or pests from one area to another.