I would say that it can only become an issue if you make it one. If you have good reasons for wanting to do the PPL bit at one school and the rest at another, I'm sure you'll be able to explain that to whoever asks. They may ask about the circumstances of you leaving the integrated school, but again, have the story ready to explain. In the end, if you have the paperwork and experience they're after, as long as you did not scrape past the exams with the bare minimums needed or used up many extra attempts at each practical exam, you should be what they're looking for.
Silly thought, why not go to one school to do the modular bits in sequence? It might make things easier on you as you would be familiar with teaching styles, instructors, the aircraft and the procedures.