I used the Pomodoro technique (25/5) when writing my Master's thesis. I had no problem settling in after my breaks. When the 25-minute work period ended, I would literally stop mid sentence, leave my text editor open, and walk outside. It was easy to get started again after my break, because I was in the middle of a sentence that needed finishing. That was usually enough to get me back up to speed, because after a 5-minute break, my mind hadn't wandered too far.
When it's time to start working again, do you start work immediately or does it take some time to get back to where you stopped?
Or do you have to design your work to be in chunks of 50 mins for this to be effective?