From practical experience, the break in the flow is minimal: you lose your immediate context, not the entire structure you've built up in your mind. And the loss of context isn't always bad, as it's helped me figure out small problems or identify potential problems which I normally miss from being constantly heads down.

I've been trying this concept for a few days and it's not that bad. It just forces me to stop typing and looking at my screen, not stop thinking or working on my problem, so it doesn't really affect my flow or concentration. It's actually kind of helpful to have to stop and think about what I'm doing.

I actually use a similar thing - I run a script that locks the screen every 30 minutes and take a short break. At first it can be a bit annoying, but it does reduce eye strain and improves overall well-being.

I use RSIGuard (Mac), not for eye strain but for muscle pain in my forearms. I've set it up to give micro breaks (10 seconds) every 5 minutes and exercise breaks (4 minutes) every 45 minutes. It does break the flow, which is a bit of a pain, but not as much of a pain as I had in my arms :-)

I've written more about how I got rid of my RSI here: http://henrikwarne.com/2012/02/18/how-i-beat-rsi/

Having pain in your wrists and fingers so you can't type, and not having the ability to focus on the screen, those things are very annoying for developers.