Hey Cristian – good question, it’s a very normal concern for many athletes when looking at swim sets.
Your first option would be to practice deep water starts when you do have multiple efforts that are only 25m long. You just put yourself in a horizontal sculling position, then accelerate your stroke rate. This not only helps you practice for a possible race day scenario, it does also teach your hands how to “feel” the increasing pressure on the water, unlike when you push off the walls, which happens to be your highest velocity in the whole lap.
Your 2nd option, for when you do something like 50m hard + 25m EZ, you can simply do 50m hard + 50m EZ. Then just note the extra volume done at the end of the session. It won’t affect the big picture in a negative way.
OR you could lower the number of reps, and do 100m hard + 50m EZ.