The 5x5 program is not a hypertrophy specific program. It’s a classic powerlifting approach and the outcomes are as follows:
1) Increased strength (at a much greater rate than with hypertrophy training)
2) Increased muscle tone and definition. Heavier weights put a greater amount of tension of the working muscles. (Muscle tone is simply resting tension on a given muscle)
3) Maximize the effects of hypertrophy training once resumed. After completing a 5x5 program; your muscles will be "primed" for great gains. When you resume a higher volume, higher rep range program; your muscle will react beautifully, as they have not been accustomed to this type of training for some time.
When you shift modes of training, you shift goals. Your mode of training needs to be customed tailored to your goals and diet. If your goal is to get lean while looking full, hard, and ripped; then the 5x5 program is a great way to achieve this. It is not very taxing on glycogen stores, and it greatly increases the amount of tension placed on the working muscles. A hypertrophy program combined with a calorically restricted diet will likely leave you lean, but also flat and soft. It is not the optimal type of training to conduct while on a cutting phase.
Another benefit of 5x5 is that if you were previously conducting a higher volume, higher rep range type of training (which seems to be the case from your post) then your muscle will be quite shocked by the lower rep range. You may end up even putting on a few pounds of lean mass despite the calorie restriction. Even if calories are not high enough to promote growth; you will still be able to retain more lean mass using this approach.
All in all, the training will not "set you back," but it will bump you forward in a variety of ways. Don't worry about trying to lift the same total poundage as you did while training for hypertrophy; your goals have changed, thus your workout regimen needs to change. It's like comparing apples and oranges. Two totally different things, with two completely different objectives.
One last thing. I have seen individuals do the 5x5 program with 2 exercises per body part for a total of ~50 reps. Obviously this allows for a greater tonnage to be lifted. This particular approach is fine provided that calories are moderatly restricted, but it is quite time consuming. I would not recommend doing this with severe caloric restrictions; and to be honest, I don't believe that it is even neccesary with more moderate-type diets.